Starting phenix.real_space_refine
on Fri Aug 22 14:21:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4c_18885/08_2025/8r4c_18885.map"
  }
  resolution = 3.55
  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=   0.000 sd=   0.140
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    2541      2.51       5
     N     669      2.21       5
     O     808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4027
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 843
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3184
          Classifications: {'peptide': 437}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 22, 'TRANS': 414}
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 205
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 5, 'GLU:plan': 13, 'ASP:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 95
  Time building chain proxies: 0.93, per 1000 atoms: 0.23
  Number of scatterers: 4027
  At special positions: 0
  Unit cell: (54.6476, 73.3429, 104.981, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       9     16.00
     O     808      8.00
     N     669      7.00
     C    2541      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 173.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1054

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 6 sheets defined
      19.7% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.848A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 15
    Processing helix  chain 'A' and resid 51 through 62
      removed outlier: 3.736A  pdb=" N   ILE A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN A  57 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      Proline residue:  A  58  - end of helix
      removed outlier: 3.617A  pdb=" N   LEU A  62 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 4.089A  pdb=" N   SER A 127 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 150
      removed outlier: 3.522A  pdb=" N   SER A 149 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 172
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 4.089A  pdb=" N   GLU A 214 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.904A  pdb=" N   SER A 237 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 260
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 320 through 324
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.740A  pdb=" N   LEU A 345 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 392
    Processing helix  chain 'A' and resid 419 through 426
      removed outlier: 3.790A  pdb=" N   GLY A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 439
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL C  33 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   MET C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   SER C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   GLY C  99 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ASN C 107 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ILE C 101 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   TYR C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 20
      removed outlier: 6.297A  pdb=" N   GLU A  19 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A  30 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA A  41 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A 222 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267
      removed outlier: 6.842A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 333 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377
      removed outlier: 6.411A  pdb=" N   GLU A 396 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    240 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: 0.51

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1323
        1.34 -     1.46: 526
        1.46 -     1.57: 2222
        1.57 -     1.69: 0
        1.69 -     1.81: 15
  Bond restraints: 4086
  Sorted by residual:
  bond pdb=" N   PRO A 414 "
       pdb=" CA  PRO A 414 "
    ideal  model  delta    sigma   weight residual
    1.469  1.485 -0.016 1.28e-02 6.10e+03 1.57e+00
  bond pdb=" CB  ILE A 144 "
       pdb=" CG1 ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.024 2.00e-02 2.50e+03 1.42e+00
  bond pdb=" CA  ILE A 144 "
       pdb=" CB  ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.540  1.556 -0.016 1.36e-02 5.41e+03 1.40e+00
  bond pdb=" CB  VAL C  48 "
       pdb=" CG2 VAL C  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.92e-01
  bond pdb=" CB  CYS C  95 "
       pdb=" SG  CYS C  95 "
    ideal  model  delta    sigma   weight residual
    1.808  1.780  0.028 3.30e-02 9.18e+02 7.39e-01
  ... (remaining 4081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 5359
        1.54 -     3.08: 174
        3.08 -     4.63: 38
        4.63 -     6.17: 11
        6.17 -     7.71: 5
  Bond angle restraints: 5587
  Sorted by residual:
  angle pdb=" N   ILE A 166 "
        pdb=" CA  ILE A 166 "
        pdb=" C   ILE A 166 "
      ideal   model   delta    sigma   weight residual
     113.20  109.27    3.93 9.60e-01 1.09e+00 1.68e+01
  angle pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
        pdb=" CD1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  121.51   -7.71 2.10e+00 2.27e-01 1.35e+01
  angle pdb=" CA  ILE A 144 "
        pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     110.40  116.38   -5.98 1.70e+00 3.46e-01 1.24e+01
  angle pdb=" CA  GLN A  12 "
        pdb=" CB  GLN A  12 "
        pdb=" CG  GLN A  12 "
      ideal   model   delta    sigma   weight residual
     114.10  120.42   -6.32 2.00e+00 2.50e-01 9.99e+00
  angle pdb=" N   ALA C  91 "
        pdb=" CA  ALA C  91 "
        pdb=" C   ALA C  91 "
      ideal   model   delta    sigma   weight residual
     108.34  112.10   -3.76 1.31e+00 5.83e-01 8.24e+00
  ... (remaining 5582 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 2071
       16.71 -    33.43: 319
       33.43 -    50.14: 88
       50.14 -    66.85: 16
       66.85 -    83.56: 7
  Dihedral angle restraints: 2501
    sinusoidal: 886
      harmonic: 1615
  Sorted by residual:
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  95 "
           pdb=" CB  CYS C  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.85  -74.85     1      1.00e+01 1.00e-02 7.09e+01
  dihedral pdb=" CA  LYS A 173 "
           pdb=" C   LYS A 173 "
           pdb=" N   SER A 174 "
           pdb=" CA  SER A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  SER A 203 "
           pdb=" C   SER A 203 "
           pdb=" N   SER A 204 "
           pdb=" CA  SER A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 2498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 417
       0.033 -    0.066: 196
       0.066 -    0.099: 61
       0.099 -    0.131: 25
       0.131 -    0.164: 2
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" CA  ILE A 408 "
            pdb=" N   ILE A 408 "
            pdb=" C   ILE A 408 "
            pdb=" CB  ILE A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE A 144 "
            pdb=" CA  ILE A 144 "
            pdb=" CG1 ILE A 144 "
            pdb=" CG2 ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE A 210 "
            pdb=" N   ILE A 210 "
            pdb=" C   ILE A 210 "
            pdb=" CB  ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 698 not shown)

  Planarity restraints: 715
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 413 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.51e+00
        pdb=" N   PRO A 414 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 189 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO A 190 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 190 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 190 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 233 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 234 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 712 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 404
        2.75 -     3.28: 3926
        3.28 -     3.82: 6653
        3.82 -     4.36: 8050
        4.36 -     4.90: 13681
  Nonbonded interactions: 32714
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C  32 "
            pdb=" OH  TYR A  45 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   SER A 417 "
            pdb=" OH  TYR A 433 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A 154 "
            pdb=" OE1 GLU A 155 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   SER A 352 "
            pdb=" OG1 THR A 374 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER A 286 "
            pdb=" OG1 THR A 308 "
     model   vdw
     2.301 3.040
  ... (remaining 32709 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.010
  Find NCS groups from input model:        0.010
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4087  Z= 0.155
  Angle     :  0.718   7.710   5589  Z= 0.378
  Chirality :  0.044   0.164    701
  Planarity :  0.005   0.047    715
  Dihedral  : 17.999  83.565   1444
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 36.28 %
    Favored  : 62.56 %
  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: -2.95 (0.34), residues: 549
  helix: -1.38 (0.57), residues: 95
  sheet: -1.81 (0.43), residues: 135
  loop : -2.26 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 270 
 TYR   0.011   0.001   TYR C  37 
 PHE   0.014   0.002   PHE A 410 
 TRP   0.026   0.002   TRP C  36 
 HIS   0.001   0.000   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4086)
  covalent geometry    : angle       0.71783 ( 5587)
  SS BOND              : bond        0.00567 (    1)
  SS BOND              : angle       1.78132 (    2)
  hydrogen bonds       : bond        0.11968 (  107)
  hydrogen bonds       : angle       5.52016 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  214 GLU cc_start: 0.6355 (mp0) cc_final: 0.6038 (mp0)
REVERT: A  376 PHE cc_start: 0.8570 (t80) cc_final: 0.8106 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 129
  average time/residue: 0.0663
  time to fit residues: 10.5547
Evaluate side-chains
  129 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.134683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.112339 restraints weight = 5622.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.115186 restraints weight = 3254.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.117176 restraints weight = 2303.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.118359 restraints weight = 1837.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.119068 restraints weight = 1587.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.0654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4087  Z= 0.141
  Angle     :  0.654   6.807   5589  Z= 0.333
  Chirality :  0.043   0.182    701
  Planarity :  0.005   0.043    715
  Dihedral  :  5.519  35.896    583
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 30.93 %
    Favored  : 62.56 %
  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: -2.87 (0.34), residues: 549
  helix: -1.26 (0.56), residues: 102
  sheet: -1.80 (0.44), residues: 129
  loop : -2.22 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 270 
 TYR   0.007   0.001   TYR C  94 
 PHE   0.015   0.002   PHE A 410 
 TRP   0.015   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4086)
  covalent geometry    : angle       0.65351 ( 5587)
  SS BOND              : bond        0.00632 (    1)
  SS BOND              : angle       1.61751 (    2)
  hydrogen bonds       : bond        0.04451 (  107)
  hydrogen bonds       : angle       4.81503 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.156 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7150 (tp40) cc_final: 0.6006 (tp40)
REVERT: C   45 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7279 (mtt180)
REVERT: A  214 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5794 (mp0)
REVERT: A  257 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5507 (tt)
REVERT: A  301 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7200 (tt)
REVERT: A  338 GLN cc_start: 0.7889 (mp10) cc_final: 0.7439 (mp10)
  outliers start: 28
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0616
  time to fit residues: 10.7776
Evaluate side-chains
  145 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.134655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.112395 restraints weight = 5553.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.115330 restraints weight = 3229.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.117265 restraints weight = 2276.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.118379 restraints weight = 1819.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.119244 restraints weight = 1580.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.0841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4087  Z= 0.146
  Angle     :  0.660   8.452   5589  Z= 0.332
  Chirality :  0.043   0.180    701
  Planarity :  0.005   0.044    715
  Dihedral  :  5.339  47.290    576
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 29.53 %
    Favored  : 62.79 %
  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: -2.85 (0.34), residues: 549
  helix: -1.24 (0.56), residues: 102
  sheet: -1.85 (0.45), residues: 130
  loop : -2.18 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  54 
 TYR   0.007   0.001   TYR C  94 
 PHE   0.014   0.002   PHE A 410 
 TRP   0.013   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4086)
  covalent geometry    : angle       0.65996 ( 5587)
  SS BOND              : bond        0.00553 (    1)
  SS BOND              : angle       1.51785 (    2)
  hydrogen bonds       : bond        0.04445 (  107)
  hydrogen bonds       : angle       4.71593 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.177 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7250 (tp40) cc_final: 0.6948 (tp40)
REVERT: C   45 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7380 (mtt180)
REVERT: A   13 GLU cc_start: 0.7093 (tp30) cc_final: 0.6804 (tp30)
REVERT: A  155 GLU cc_start: 0.8267 (mp0) cc_final: 0.7868 (mp0)
REVERT: A  214 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5756 (mp0)
REVERT: A  257 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5555 (tt)
REVERT: A  301 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7128 (tt)
REVERT: A  338 GLN cc_start: 0.7900 (mp10) cc_final: 0.7478 (mp10)
  outliers start: 33
  outliers final: 24
  residues processed: 139
  average time/residue: 0.0695
  time to fit residues: 11.9544
Evaluate side-chains
  151 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 34 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.133979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.111720 restraints weight = 5566.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.114633 restraints weight = 3249.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.116523 restraints weight = 2295.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.117629 restraints weight = 1849.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.118544 restraints weight = 1611.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4087  Z= 0.157
  Angle     :  0.673   7.532   5589  Z= 0.337
  Chirality :  0.044   0.175    701
  Planarity :  0.005   0.041    715
  Dihedral  :  5.540  57.441    576
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  9.77 %
    Allowed  : 28.84 %
    Favored  : 61.40 %
  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: -2.72 (0.35), residues: 549
  helix: -1.07 (0.60), residues: 95
  sheet: -1.87 (0.45), residues: 130
  loop : -2.04 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 270 
 TYR   0.007   0.001   TYR C  94 
 PHE   0.016   0.002   PHE A 115 
 TRP   0.013   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4086)
  covalent geometry    : angle       0.67288 ( 5587)
  SS BOND              : bond        0.00589 (    1)
  SS BOND              : angle       1.57070 (    2)
  hydrogen bonds       : bond        0.04531 (  107)
  hydrogen bonds       : angle       4.71757 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.159 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7219 (tp40) cc_final: 0.6863 (tp40)
REVERT: C   45 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7322 (mtt180)
REVERT: A   29 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7705 (mttt)
REVERT: A   54 ARG cc_start: 0.7640 (mtm110) cc_final: 0.6929 (ttp80)
REVERT: A  257 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5548 (tt)
REVERT: A  301 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7105 (tt)
REVERT: A  338 GLN cc_start: 0.7855 (mp-120) cc_final: 0.7389 (mp10)
  outliers start: 42
  outliers final: 30
  residues processed: 145
  average time/residue: 0.0674
  time to fit residues: 12.1085
Evaluate side-chains
  156 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.132518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.110153 restraints weight = 5592.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.113037 restraints weight = 3253.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.114751 restraints weight = 2298.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.116136 restraints weight = 1854.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.116841 restraints weight = 1600.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4087  Z= 0.167
  Angle     :  0.677   6.990   5589  Z= 0.339
  Chirality :  0.044   0.173    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.566  54.914    576
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  9.53 %
    Allowed  : 29.07 %
    Favored  : 61.40 %
  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: -2.85 (0.35), residues: 549
  helix: -1.21 (0.58), residues: 102
  sheet: -1.88 (0.45), residues: 130
  loop : -2.17 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 270 
 TYR   0.007   0.001   TYR C  94 
 PHE   0.015   0.002   PHE A 115 
 TRP   0.013   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 4086)
  covalent geometry    : angle       0.67629 ( 5587)
  SS BOND              : bond        0.00632 (    1)
  SS BOND              : angle       1.64997 (    2)
  hydrogen bonds       : bond        0.04619 (  107)
  hydrogen bonds       : angle       4.71081 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7202 (tp40) cc_final: 0.6855 (tp40)
REVERT: C   45 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7021 (mtt180)
REVERT: A  155 GLU cc_start: 0.8311 (mp0) cc_final: 0.7928 (mp0)
REVERT: A  257 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5706 (tt)
REVERT: A  301 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7052 (tt)
REVERT: A  338 GLN cc_start: 0.7902 (mp-120) cc_final: 0.7468 (mp10)
REVERT: A  374 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.6882 (p)
  outliers start: 41
  outliers final: 31
  residues processed: 149
  average time/residue: 0.0668
  time to fit residues: 12.3917
Evaluate side-chains
  157 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.134968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.112682 restraints weight = 5658.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.115600 restraints weight = 3233.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.117545 restraints weight = 2263.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.118897 restraints weight = 1794.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.119545 restraints weight = 1542.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4087  Z= 0.133
  Angle     :  0.656   6.979   5589  Z= 0.328
  Chirality :  0.043   0.175    701
  Planarity :  0.005   0.041    715
  Dihedral  :  5.255  44.956    576
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  8.84 %
    Allowed  : 29.30 %
    Favored  : 61.86 %
  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: -2.83 (0.35), residues: 549
  helix: -1.23 (0.58), residues: 102
  sheet: -1.85 (0.45), residues: 131
  loop : -2.15 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 270 
 TYR   0.006   0.001   TYR C  37 
 PHE   0.015   0.002   PHE A 115 
 TRP   0.014   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4086)
  covalent geometry    : angle       0.65560 ( 5587)
  SS BOND              : bond        0.00518 (    1)
  SS BOND              : angle       1.52815 (    2)
  hydrogen bonds       : bond        0.04147 (  107)
  hydrogen bonds       : angle       4.61459 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.193 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7288 (tp40) cc_final: 0.6887 (tp40)
REVERT: C   45 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.6998 (mtt180)
REVERT: C   89 ASP cc_start: 0.8058 (m-30) cc_final: 0.7857 (m-30)
REVERT: A   54 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6556 (ttp80)
REVERT: A  155 GLU cc_start: 0.8300 (mp0) cc_final: 0.7868 (mp0)
REVERT: A  257 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5395 (tt)
REVERT: A  301 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7177 (tt)
REVERT: A  338 GLN cc_start: 0.7806 (mp-120) cc_final: 0.7377 (mp10)
  outliers start: 38
  outliers final: 33
  residues processed: 146
  average time/residue: 0.0713
  time to fit residues: 12.9271
Evaluate side-chains
  161 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.134918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.112488 restraints weight = 5710.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.115253 restraints weight = 3234.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.117220 restraints weight = 2279.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.118623 restraints weight = 1821.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.119389 restraints weight = 1557.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4087  Z= 0.138
  Angle     :  0.655   6.773   5589  Z= 0.326
  Chirality :  0.043   0.173    701
  Planarity :  0.005   0.041    715
  Dihedral  :  5.110  36.919    576
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  9.07 %
    Allowed  : 29.07 %
    Favored  : 61.86 %
  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: -2.80 (0.35), residues: 549
  helix: -1.20 (0.58), residues: 102
  sheet: -1.80 (0.45), residues: 131
  loop : -2.15 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 270 
 TYR   0.006   0.001   TYR C  37 
 PHE   0.014   0.002   PHE A 115 
 TRP   0.015   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4086)
  covalent geometry    : angle       0.65402 ( 5587)
  SS BOND              : bond        0.00539 (    1)
  SS BOND              : angle       1.52674 (    2)
  hydrogen bonds       : bond        0.04206 (  107)
  hydrogen bonds       : angle       4.60290 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 126
  time to evaluate  : 0.098 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7286 (tp40) cc_final: 0.6788 (tp40)
REVERT: C   45 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7235 (mtt180)
REVERT: C   56 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7402 (mtm180)
REVERT: A   13 GLU cc_start: 0.7059 (tp30) cc_final: 0.6851 (tp30)
REVERT: A   54 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6545 (ttp80)
REVERT: A  155 GLU cc_start: 0.8296 (mp0) cc_final: 0.7834 (mp0)
REVERT: A  257 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5511 (tt)
REVERT: A  301 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7180 (tt)
REVERT: A  338 GLN cc_start: 0.7907 (mp-120) cc_final: 0.7447 (mp10)
  outliers start: 39
  outliers final: 35
  residues processed: 148
  average time/residue: 0.0660
  time to fit residues: 12.1214
Evaluate side-chains
  164 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.133725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.111502 restraints weight = 5612.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.114359 restraints weight = 3227.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.116317 restraints weight = 2263.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.117416 restraints weight = 1807.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.118283 restraints weight = 1570.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4087  Z= 0.155
  Angle     :  0.676   7.221   5589  Z= 0.336
  Chirality :  0.044   0.174    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.160  34.074    576
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers : 10.23 %
    Allowed  : 28.14 %
    Favored  : 61.63 %
  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: -2.71 (0.35), residues: 549
  helix: -1.09 (0.61), residues: 95
  sheet: -1.81 (0.45), residues: 131
  loop : -2.05 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 270 
 TYR   0.006   0.001   TYR C  94 
 PHE   0.013   0.002   PHE A 115 
 TRP   0.017   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4086)
  covalent geometry    : angle       0.67556 ( 5587)
  SS BOND              : bond        0.00578 (    1)
  SS BOND              : angle       1.53831 (    2)
  hydrogen bonds       : bond        0.04403 (  107)
  hydrogen bonds       : angle       4.66862 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 129
  time to evaluate  : 0.166 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7278 (tp40) cc_final: 0.6769 (tp40)
REVERT: C   45 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7239 (mtt180)
REVERT: A   54 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6550 (ttp80)
REVERT: A  144 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7395 (pp)
REVERT: A  257 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5599 (tt)
REVERT: A  301 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7070 (tt)
REVERT: A  338 GLN cc_start: 0.7917 (mp-120) cc_final: 0.7545 (mp10)
  outliers start: 44
  outliers final: 37
  residues processed: 154
  average time/residue: 0.0675
  time to fit residues: 12.9035
Evaluate side-chains
  166 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0070
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.133831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.111423 restraints weight = 5724.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.114327 restraints weight = 3263.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.116348 restraints weight = 2281.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.117639 restraints weight = 1794.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.118220 restraints weight = 1545.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4087  Z= 0.151
  Angle     :  0.673   7.049   5589  Z= 0.335
  Chirality :  0.043   0.173    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.123  32.150    576
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  9.53 %
    Allowed  : 29.53 %
    Favored  : 60.93 %
  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: -2.80 (0.35), residues: 549
  helix: -1.18 (0.58), residues: 102
  sheet: -1.76 (0.45), residues: 131
  loop : -2.18 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 270 
 TYR   0.006   0.001   TYR C  37 
 PHE   0.014   0.002   PHE A 115 
 TRP   0.020   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4086)
  covalent geometry    : angle       0.67231 ( 5587)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       1.58916 (    2)
  hydrogen bonds       : bond        0.04337 (  107)
  hydrogen bonds       : angle       4.61056 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.169 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7268 (tp40) cc_final: 0.6749 (tp40)
REVERT: C   45 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7231 (mtt180)
REVERT: A   54 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6457 (ttp80)
REVERT: A  144 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7366 (pp)
REVERT: A  155 GLU cc_start: 0.8272 (mp0) cc_final: 0.7944 (mp0)
REVERT: A  214 GLU cc_start: 0.5827 (mp0) cc_final: 0.5447 (mp0)
REVERT: A  257 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5779 (tt)
REVERT: A  301 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7160 (tt)
REVERT: A  338 GLN cc_start: 0.7910 (mp-120) cc_final: 0.7483 (mp10)
  outliers start: 41
  outliers final: 38
  residues processed: 149
  average time/residue: 0.0640
  time to fit residues: 11.9534
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 3 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.134260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.112061 restraints weight = 5577.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.114942 restraints weight = 3206.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.116810 restraints weight = 2257.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.118130 restraints weight = 1804.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.118435 restraints weight = 1555.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4087  Z= 0.152
  Angle     :  0.679   7.239   5589  Z= 0.338
  Chirality :  0.044   0.172    701
  Planarity :  0.005   0.042    715
  Dihedral  :  5.147  31.282    576
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  9.77 %
    Allowed  : 28.84 %
    Favored  : 61.40 %
  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: -2.72 (0.35), residues: 549
  helix: -1.06 (0.61), residues: 95
  sheet: -1.79 (0.45), residues: 131
  loop : -2.08 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 270 
 TYR   0.006   0.001   TYR C  94 
 PHE   0.014   0.002   PHE A 115 
 TRP   0.021   0.001   TRP C  36 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4086)
  covalent geometry    : angle       0.67806 ( 5587)
  SS BOND              : bond        0.00577 (    1)
  SS BOND              : angle       1.60878 (    2)
  hydrogen bonds       : bond        0.04350 (  107)
  hydrogen bonds       : angle       4.62397 (  240)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.107 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7267 (tp40) cc_final: 0.6753 (tp40)
REVERT: C   45 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7231 (mtt180)
REVERT: A   54 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6436 (ttp80)
REVERT: A  144 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7358 (pp)
REVERT: A  155 GLU cc_start: 0.8261 (mp0) cc_final: 0.7914 (mp0)
REVERT: A  214 GLU cc_start: 0.5814 (mp0) cc_final: 0.5436 (mp0)
REVERT: A  257 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5468 (tt)
REVERT: A  301 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7164 (tt)
REVERT: A  338 GLN cc_start: 0.7911 (mp-120) cc_final: 0.7547 (mp10)
  outliers start: 42
  outliers final: 37
  residues processed: 150
  average time/residue: 0.0595
  time to fit residues: 11.3073
Evaluate side-chains
  168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   95 CYS
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0020
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0870
   chunk 40 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.4166

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.136394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.114169 restraints weight = 5581.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.117098 restraints weight = 3201.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.119020 restraints weight = 2246.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.120150 restraints weight = 1784.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.121138 restraints weight = 1547.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4087  Z= 0.125
  Angle     :  0.648   6.904   5589  Z= 0.322
  Chirality :  0.043   0.171    701
  Planarity :  0.005   0.041    715
  Dihedral  :  4.956  27.188    576
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  8.84 %
    Allowed  : 30.00 %
    Favored  : 61.16 %
  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: -2.68 (0.35), residues: 549
  helix: -1.24 (0.58), residues: 103
  sheet: -1.80 (0.46), residues: 131
  loop : -1.98 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 270 
 TYR   0.007   0.001   TYR C  37 
 PHE   0.015   0.002   PHE A 115 
 TRP   0.022   0.001   TRP C  36 
 HIS   0.001   0.000   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4086)
  covalent geometry    : angle       0.64772 ( 5587)
  SS BOND              : bond        0.00453 (    1)
  SS BOND              : angle       1.47360 (    2)
  hydrogen bonds       : bond        0.03929 (  107)
  hydrogen bonds       : angle       4.54244 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 815.26 seconds
wall clock time: 14 minutes 41.62 seconds (881.62 seconds total)