Starting phenix.real_space_refine
on Fri May  9 17:34:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ws7_37800/05_2025/8ws7_37800.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      54      5.49       5
     S       3      5.16       5
     C    1934      2.51       5
     N     604      2.21       5
     O     738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3333
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2207
          Classifications: {'peptide': 279}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 251}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 360
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 627
          Classifications: {'RNA': 30}
          Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 10, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 6, 'rna3p': 23}
    Chain: "D"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 139
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 3.96, per 1000 atoms: 1.19
  Number of scatterers: 3333
  At special positions: 0
  Unit cell: (54.78, 77.88, 91.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       3     16.00
     P      54     15.00
     O     738      8.00
     N     604      7.00
     C    1934      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.07
  Conformation dependent library (CDL) restraints added in 247.4 milliseconds
  

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  508

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 1 sheets defined
      38.0% alpha, 7.9% beta
      9 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 89
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 4.087A  pdb=" N   GLU A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 3.654A  pdb=" N   PHE A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 158
      removed outlier: 3.582A  pdb=" N   ILE A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 134 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   HIS A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 143 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A 144 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.534A  pdb=" N   ARG A 251 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 292
      removed outlier: 3.559A  pdb=" N   LEU A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLU A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 319
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 333 through 335
      No H-bonds generated for 'chain 'A' and resid 333 through 335'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199
      removed outlier: 3.684A  pdb=" N   ILE A 198 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE A 347 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLN A  68 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE A 296 " --> pdb=" O   MET A 307 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    207 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 774
        1.33 -     1.45: 971
        1.45 -     1.57: 1670
        1.57 -     1.69: 105
        1.69 -     1.81: 4
  Bond restraints: 3524
  Sorted by residual:
  bond pdb=" CA  LYS A 273 "
       pdb=" C   LYS A 273 "
    ideal  model  delta    sigma   weight residual
    1.522  1.561 -0.039 1.06e-02 8.90e+03 1.33e+01
  bond pdb=" CA  ARG A  70 "
       pdb=" C   ARG A  70 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 1.01e-02 9.80e+03 7.89e+00
  bond pdb=" C   ARG A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.330  1.363 -0.033 1.22e-02 6.72e+03 7.24e+00
  bond pdb=" C   LYS A 273 "
       pdb=" N   PRO A 274 "
    ideal  model  delta    sigma   weight residual
    1.333  1.366 -0.032 1.44e-02 4.82e+03 5.08e+00
  bond pdb=" CA  PHE A 335 "
       pdb=" C   PHE A 335 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.19e-02 7.06e+03 1.84e+00
  ... (remaining 3519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 4796
        1.45 -     2.90: 185
        2.90 -     4.35: 28
        4.35 -     5.80: 4
        5.80 -     7.25: 2
  Bond angle restraints: 5015
  Sorted by residual:
  angle pdb=" N   LEU A  72 "
        pdb=" CA  LEU A  72 "
        pdb=" C   LEU A  72 "
      ideal   model   delta    sigma   weight residual
     113.01  117.65   -4.64 1.20e+00 6.94e-01 1.50e+01
  angle pdb=" C   ARG A  70 "
        pdb=" CA  ARG A  70 "
        pdb=" CB  ARG A  70 "
      ideal   model   delta    sigma   weight residual
     109.22  113.64   -4.42 1.52e+00 4.33e-01 8.47e+00
  angle pdb=" CA  SER A  69 "
        pdb=" C   SER A  69 "
        pdb=" N   ARG A  70 "
      ideal   model   delta    sigma   weight residual
     117.17  114.05    3.12 1.18e+00 7.18e-01 6.97e+00
  angle pdb=" O   SER A  69 "
        pdb=" C   SER A  69 "
        pdb=" N   ARG A  70 "
      ideal   model   delta    sigma   weight residual
     122.09  124.72   -2.63 1.08e+00 8.57e-01 5.92e+00
  angle pdb=" N   TYR A 140 "
        pdb=" CA  TYR A 140 "
        pdb=" C   TYR A 140 "
      ideal   model   delta    sigma   weight residual
     111.07  108.81    2.26 1.07e+00 8.73e-01 4.46e+00
  ... (remaining 5010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.05: 1926
       34.05 -    68.10: 172
       68.10 -   102.14: 17
      102.14 -   136.19: 0
      136.19 -   170.24: 2
  Dihedral angle restraints: 2117
    sinusoidal: 1322
      harmonic: 795
  Sorted by residual:
  dihedral pdb=" O4'   U B  10 "
           pdb=" C1'   U B  10 "
           pdb=" N1    U B  10 "
           pdb=" C2    U B  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   58.25  141.75     1      1.50e+01 4.44e-03 7.62e+01
  dihedral pdb=" O4'   U B  -9 "
           pdb=" C1'   U B  -9 "
           pdb=" N1    U B  -9 "
           pdb=" C2    U B  -9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   61.76  170.24     1      1.70e+01 3.46e-03 6.60e+01
  dihedral pdb=" CA  TRP A 318 "
           pdb=" C   TRP A 318 "
           pdb=" N   ARG A 319 "
           pdb=" CA  ARG A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 2114 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 484
       0.052 -    0.103: 62
       0.103 -    0.155: 22
       0.155 -    0.206: 1
       0.206 -    0.258: 2
  Chirality restraints: 571
  Sorted by residual:
  chirality pdb=" CA  LEU A  72 "
            pdb=" N   LEU A  72 "
            pdb=" C   LEU A  72 "
            pdb=" CB  LEU A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE A 198 "
            pdb=" N   ILE A 198 "
            pdb=" C   ILE A 198 "
            pdb=" CB  ILE A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  LYS A 273 "
            pdb=" N   LYS A 273 "
            pdb=" C   LYS A 273 "
            pdb=" CB  LYS A 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.92e-01
  ... (remaining 568 not shown)

  Planarity restraints: 450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  70 "   -0.040 5.00e-02 4.00e+02   6.19e-02 6.13e+00
        pdb=" N   PRO A  71 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  69 "    0.009 2.00e-02 2.50e+03   1.92e-02 3.68e+00
        pdb=" C   SER A  69 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   SER A  69 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A  70 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  75 "   -0.029 5.00e-02 4.00e+02   4.40e-02 3.10e+00
        pdb=" N   PRO A  76 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 447 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 809
        2.80 -     3.32: 2904
        3.32 -     3.85: 5913
        3.85 -     4.37: 7050
        4.37 -     4.90: 10629
  Nonbonded interactions: 27305
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 127 "
            pdb=" O4   DT D  -2 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" NH1 ARG A 260 "
            pdb=" O6    G B -16 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" O2'   C B  -6 "
            pdb=" OP2   C B  -5 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O6   DG C   5 "
            pdb=" N4   DC D  -6 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" N6   DA C -10 "
            pdb=" O4    U B  10 "
     model   vdw
     2.425 3.120
  ... (remaining 27300 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 individual isotropic
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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.960
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
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   0.039   3524  Z= 0.196
  Angle     :  0.646   7.250   5015  Z= 0.370
  Chirality :  0.042   0.258    571
  Planarity :  0.006   0.062    450
  Dihedral  : 21.449 170.241   1609
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  1.72 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.50), residues: 275
  helix: -1.23 (0.51), residues: 98
  sheet:  0.58 (1.11), residues: 26
  loop : -0.78 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 318 
 HIS   0.002   0.001   HIS A 253 
 PHE   0.009   0.001   PHE A 334 
 TYR   0.006   0.001   TYR A 201 
 ARG   0.004   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25870 (   94)
  hydrogen bonds       : angle       9.73398 (  247)
  covalent geometry    : bond        0.00352 ( 3524)
  covalent geometry    : angle       0.64627 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6449 (mp0) cc_final: 0.6114 (mp0)
REVERT: A  302 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7761 (mtpp)
  outliers start: 2
  outliers final: 1
  residues processed: 31
  average time/residue: 0.3585
  time to fit residues: 12.3801
Evaluate side-chains
  26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    0.0370
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.2256

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.145662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130396 restraints weight = 4841.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.29
r_work: 0.3549 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3524  Z= 0.139
  Angle     :  0.595   7.315   5015  Z= 0.316
  Chirality :  0.039   0.136    571
  Planarity :  0.005   0.034    450
  Dihedral  : 23.546 170.042   1055
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.19 %
    Favored  : 91.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.49), residues: 275
  helix: -0.57 (0.50), residues: 102
  sheet:  0.33 (0.97), residues: 33
  loop : -0.62 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.008   0.001   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.003   0.000   ARG A 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04483 (   94)
  hydrogen bonds       : angle       4.97940 (  247)
  covalent geometry    : bond        0.00301 ( 3524)
  covalent geometry    : angle       0.59498 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6855 (mp0) cc_final: 0.6529 (mp0)
REVERT: A  150 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6937 (mtm-85)
REVERT: A  302 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8212 (mtpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.3077
  time to fit residues: 11.5231
Evaluate side-chains
  29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 23 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.3138

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.144411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129244 restraints weight = 4803.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.34
r_work: 0.3515 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3524  Z= 0.146
  Angle     :  0.577   7.075   5015  Z= 0.303
  Chirality :  0.039   0.139    571
  Planarity :  0.005   0.034    450
  Dihedral  : 23.249 170.176   1051
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.34 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.50), residues: 275
  helix: -0.35 (0.51), residues: 102
  sheet:  0.24 (0.96), residues: 33
  loop : -0.48 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 112 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.011   0.002   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.006   0.001   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (   94)
  hydrogen bonds       : angle       4.63468 (  247)
  covalent geometry    : bond        0.00318 ( 3524)
  covalent geometry    : angle       0.57747 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6996 (mp0) cc_final: 0.6555 (mp0)
REVERT: A  302 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8235 (mtpp)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.2843
  time to fit residues: 9.8664
Evaluate side-chains
  29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    0.1980
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.141206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125986 restraints weight = 4887.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.34
r_work: 0.3472 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3524  Z= 0.241
  Angle     :  0.667   7.369   5015  Z= 0.347
  Chirality :  0.044   0.160    571
  Planarity :  0.006   0.041    450
  Dihedral  : 23.436 170.053   1051
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.09 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.49), residues: 275
  helix: -0.44 (0.51), residues: 102
  sheet: -0.64 (0.98), residues: 28
  loop : -0.60 (0.50), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 270 
 HIS   0.004   0.002   HIS A 214 
 PHE   0.018   0.003   PHE A 350 
 TYR   0.011   0.002   TYR A  89 
 ARG   0.006   0.001   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (   94)
  hydrogen bonds       : angle       4.86328 (  247)
  covalent geometry    : bond        0.00534 ( 3524)
  covalent geometry    : angle       0.66718 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7148 (mp0) cc_final: 0.6558 (mp0)
REVERT: A  302 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8339 (mtpp)
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.2509
  time to fit residues: 10.4543
Evaluate side-chains
  33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  264 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.140821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.125409 restraints weight = 4921.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.30
r_work: 0.3487 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3524  Z= 0.196
  Angle     :  0.601   6.836   5015  Z= 0.316
  Chirality :  0.040   0.151    571
  Planarity :  0.006   0.040    450
  Dihedral  : 23.304 170.227   1051
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.81 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.48), residues: 275
  helix: -0.40 (0.49), residues: 104
  sheet: -0.42 (0.89), residues: 33
  loop : -0.67 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 112 
 HIS   0.003   0.001   HIS A 253 
 PHE   0.015   0.002   PHE A 350 
 TYR   0.007   0.002   TYR A 201 
 ARG   0.003   0.001   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (   94)
  hydrogen bonds       : angle       4.65649 (  247)
  covalent geometry    : bond        0.00434 ( 3524)
  covalent geometry    : angle       0.60055 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7083 (mp0) cc_final: 0.6538 (mp0)
REVERT: A  111 ARG cc_start: 0.7229 (ptm-80) cc_final: 0.6755 (ptt90)
REVERT: A  302 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8302 (mtpp)
  outliers start: 6
  outliers final: 4
  residues processed: 35
  average time/residue: 0.2652
  time to fit residues: 10.6709
Evaluate side-chains
  34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  264 TRP
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   chunk 6 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.142122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126554 restraints weight = 4966.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.31
r_work: 0.3502 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3524  Z= 0.153
  Angle     :  0.560   6.473   5015  Z= 0.296
  Chirality :  0.039   0.139    571
  Planarity :  0.005   0.040    450
  Dihedral  : 23.186 170.749   1051
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.67 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.49), residues: 275
  helix: -0.05 (0.50), residues: 104
  sheet: -0.34 (0.90), residues: 33
  loop : -0.57 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 112 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.012   0.002   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.002   0.000   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (   94)
  hydrogen bonds       : angle       4.43228 (  247)
  covalent geometry    : bond        0.00339 ( 3524)
  covalent geometry    : angle       0.55986 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7047 (mp0) cc_final: 0.6524 (mp0)
REVERT: A  302 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8255 (mtpp)
  outliers start: 7
  outliers final: 4
  residues processed: 37
  average time/residue: 0.2471
  time to fit residues: 10.5853
Evaluate side-chains
  35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  264 TRP
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0000
   chunk 19 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0050
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.2198

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.143597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128002 restraints weight = 4918.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.32
r_work: 0.3517 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3524  Z= 0.126
  Angle     :  0.539   6.374   5015  Z= 0.284
  Chirality :  0.037   0.131    571
  Planarity :  0.005   0.039    450
  Dihedral  : 23.078 171.115   1051
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.10 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.50), residues: 275
  helix:  0.33 (0.51), residues: 104
  sheet: -0.20 (0.93), residues: 33
  loop : -0.50 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.009   0.001   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.002   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (   94)
  hydrogen bonds       : angle       4.30168 (  247)
  covalent geometry    : bond        0.00273 ( 3524)
  covalent geometry    : angle       0.53910 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7004 (mp0) cc_final: 0.6492 (mp0)
REVERT: A  302 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8150 (mtpp)
  outliers start: 7
  outliers final: 4
  residues processed: 37
  average time/residue: 0.2547
  time to fit residues: 10.7762
Evaluate side-chains
  35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  347 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0000
   chunk 17 optimal weight:    0.0570
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0870
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.2280

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.144698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129146 restraints weight = 4814.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.28
r_work: 0.3534 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3524  Z= 0.125
  Angle     :  0.533   6.345   5015  Z= 0.280
  Chirality :  0.037   0.128    571
  Planarity :  0.005   0.038    450
  Dihedral  : 23.020 171.436   1051
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.67 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.50), residues: 275
  helix:  0.64 (0.52), residues: 104
  sheet: -0.02 (0.94), residues: 33
  loop : -0.44 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.009   0.001   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.001   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (   94)
  hydrogen bonds       : angle       4.30415 (  247)
  covalent geometry    : bond        0.00274 ( 3524)
  covalent geometry    : angle       0.53341 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6999 (mp0) cc_final: 0.6506 (mp0)
REVERT: A  302 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8140 (mtpp)
  outliers start: 9
  outliers final: 5
  residues processed: 42
  average time/residue: 0.2505
  time to fit residues: 12.1944
Evaluate side-chains
  40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  264 TRP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0020
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0070
   overall best weight:    0.2206

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.144646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128964 restraints weight = 4822.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.29
r_work: 0.3548 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3524  Z= 0.125
  Angle     :  0.555   8.628   5015  Z= 0.292
  Chirality :  0.038   0.161    571
  Planarity :  0.005   0.038    450
  Dihedral  : 22.930 172.171   1051
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.97 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.50), residues: 275
  helix:  0.70 (0.52), residues: 104
  sheet: -0.06 (1.02), residues: 28
  loop : -0.47 (0.50), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.009   0.001   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.002   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (   94)
  hydrogen bonds       : angle       4.37931 (  247)
  covalent geometry    : bond        0.00278 ( 3524)
  covalent geometry    : angle       0.55471 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6980 (mp0) cc_final: 0.6538 (mp0)
REVERT: A  302 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8122 (mtpp)
  outliers start: 8
  outliers final: 6
  residues processed: 40
  average time/residue: 0.2680
  time to fit residues: 12.3326
Evaluate side-chains
  40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  264 TRP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  327 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 26 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 25 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0030
   overall best weight:    0.2990

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.144236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.128515 restraints weight = 4765.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.27
r_work: 0.3513 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3524  Z= 0.140
  Angle     :  0.571   8.446   5015  Z= 0.299
  Chirality :  0.039   0.158    571
  Planarity :  0.005   0.038    450
  Dihedral  : 22.928 172.658   1051
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.83 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.49), residues: 275
  helix:  0.65 (0.52), residues: 104
  sheet: -0.49 (1.26), residues: 18
  loop : -0.46 (0.48), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 112 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.011   0.002   PHE A 350 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.002   0.000   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (   94)
  hydrogen bonds       : angle       4.41948 (  247)
  covalent geometry    : bond        0.00309 ( 3524)
  covalent geometry    : angle       0.57124 ( 5015)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.6995 (mp0) cc_final: 0.6544 (mp0)
REVERT: A  302 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8201 (mtpp)
  outliers start: 7
  outliers final: 7
  residues processed: 40
  average time/residue: 0.2556
  time to fit residues: 11.7121
Evaluate side-chains
  40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  264 TRP
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  327 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 8 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.142850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127235 restraints weight = 4828.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.27
r_work: 0.3490 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3524  Z= 0.180
  Angle     :  0.616   8.923   5015  Z= 0.323
  Chirality :  0.041   0.154    571
  Planarity :  0.006   0.053    450
  Dihedral  : 23.084 172.704   1051
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 18.10 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.49), residues: 275
  helix:  0.47 (0.51), residues: 104
  sheet: -0.35 (1.04), residues: 28
  loop : -0.55 (0.49), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 112 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.014   0.002   PHE A 350 
 TYR   0.008   0.001   TYR A 201 
 ARG   0.003   0.000   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (   94)
  hydrogen bonds       : angle       4.59111 (  247)
  covalent geometry    : bond        0.00402 ( 3524)
  covalent geometry    : angle       0.61583 ( 5015)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2162.67 seconds
wall clock time: 38 minutes 23.24 seconds (2303.24 seconds total)