Starting phenix.real_space_refine
on Fri Aug 22 13:45:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qt6_18644/08_2025/8qt6_18644.map"
  }
  resolution = 2.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.101
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: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       2      5.49       5
     S      11      5.16       5
     C    2261      2.51       5
     N     548      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  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: 3466
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3264
          Classifications: {'peptide': 399}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
    Chain: "A"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 202
          Unusual residues: {'FAD': 1, 'HEM': 2}
          Classifications: {'undetermined': 3, 'water': 63}
          Link IDs: {None: 65}
  Time building chain proxies: 0.95, per 1000 atoms: 0.27
  Number of scatterers: 3466
  At special positions: 0
  Unit cell: (62.1736, 67.1876, 92.2576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     S      11     16.00
     P       2     15.00
     O     642      8.00
     N     548      7.00
     C    2261      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 102.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  740

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      56.1% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 6
      No H-bonds generated for 'chain 'A' and resid 4 through 6'
    Processing helix  chain 'A' and resid 7 through 29
    Processing helix  chain 'A' and resid 32 through 48
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 61 through 88
    Processing helix  chain 'A' and resid 94 through 115
      removed outlier: 3.570A  pdb=" N   GLY A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 148
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 155 through 178
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 253 through 263
      removed outlier: 3.642A  pdb=" N   LEU A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 296 through 306
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 327 through 338
    Processing helix  chain 'A' and resid 372 through 387
      removed outlier: 3.921A  pdb=" N   ALA A 378 " --> pdb=" O   SER A 374 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 379 " --> pdb=" O   MET A 375 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236
      removed outlier: 3.708A  pdb=" N   LYS A 268 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ILE A 190 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   HIS A 206 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   HIS A 192 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347
      removed outlier: 6.865A  pdb=" N   GLN A 287 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   TYR A 316 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP A 289 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   SER A 318 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA A 291 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA A 365 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ILE A 393 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLU A 395 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   MET A 369 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)

    187 hydrogen bonds defined for protein.
    540 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: 0.39

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 1504
        1.39 -     1.56: 1981
        1.56 -     1.73: 4
        1.73 -     1.89: 21
        1.89 -     2.06: 8
  Bond restraints: 3518
  Sorted by residual:
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.588  0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.563  0.071 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.572  0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.633  1.586  0.047 2.00e-02 2.50e+03 5.51e+00
  bond pdb=" O1P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 2.00e-02 2.50e+03 3.75e+00
  ... (remaining 3513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 4683
        1.44 -     2.89: 75
        2.89 -     4.33: 27
        4.33 -     5.78: 13
        5.78 -     7.22: 3
  Bond angle restraints: 4801
  Sorted by residual:
  angle pdb=" O1P FAD A 501 "
        pdb=" P   FAD A 501 "
        pdb=" O2P FAD A 501 "
      ideal   model   delta    sigma   weight residual
     122.50  115.28    7.22 3.00e+00 1.11e-01 5.79e+00
  angle pdb=" O1A FAD A 501 "
        pdb=" PA  FAD A 501 "
        pdb=" O5B FAD A 501 "
      ideal   model   delta    sigma   weight residual
     104.10  110.80   -6.70 3.00e+00 1.11e-01 4.98e+00
  angle pdb=" CA  LEU A 187 "
        pdb=" CB  LEU A 187 "
        pdb=" CG  LEU A 187 "
      ideal   model   delta    sigma   weight residual
     116.30  123.09   -6.79 3.50e+00 8.16e-02 3.76e+00
  angle pdb=" C3B HEM A 503 "
        pdb=" CAB HEM A 503 "
        pdb=" CBB HEM A 503 "
      ideal   model   delta    sigma   weight residual
     120.00  125.65   -5.65 3.00e+00 1.11e-01 3.55e+00
  angle pdb=" CA  TYR A 275 "
        pdb=" CB  TYR A 275 "
        pdb=" CG  TYR A 275 "
      ideal   model   delta    sigma   weight residual
     113.90  117.28   -3.38 1.80e+00 3.09e-01 3.54e+00
  ... (remaining 4796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 1709
       17.72 -    35.45: 201
       35.45 -    53.17: 65
       53.17 -    70.89: 16
       70.89 -    88.62: 11
  Dihedral angle restraints: 2002
    sinusoidal: 840
      harmonic: 1162
  Sorted by residual:
  dihedral pdb=" C2D HEM A 503 "
           pdb=" C3D HEM A 503 "
           pdb=" CAD HEM A 503 "
           pdb=" CBD HEM A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.35  -75.35     2      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" C1A HEM A 503 "
           pdb=" C2A HEM A 503 "
           pdb=" CAA HEM A 503 "
           pdb=" CBA HEM A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.87  -71.87     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" C1A HEM A 502 "
           pdb=" C2A HEM A 502 "
           pdb=" CAA HEM A 502 "
           pdb=" CBA HEM A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -71.84   71.84     2      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 1999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 299
       0.028 -    0.056: 124
       0.056 -    0.085: 47
       0.085 -    0.113: 24
       0.113 -    0.141: 7
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" C2B FAD A 501 "
            pdb=" C1B FAD A 501 "
            pdb=" C3B FAD A 501 "
            pdb=" O2B FAD A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.68    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE A 203 "
            pdb=" N   ILE A 203 "
            pdb=" C   ILE A 203 "
            pdb=" CB  ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  THR A 297 "
            pdb=" N   THR A 297 "
            pdb=" C   THR A 297 "
            pdb=" CB  THR A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 498 not shown)

  Planarity restraints: 576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 361 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 362 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  43 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   SER A  43 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   SER A  43 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A  44 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  41 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.65e+00
        pdb=" C   SER A  41 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER A  41 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A  42 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 573 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 137
        2.72 -     3.26: 3332
        3.26 -     3.81: 6257
        3.81 -     4.35: 8020
        4.35 -     4.90: 12844
  Nonbonded interactions: 30590
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 129 "
            pdb="FE   HEM A 503 "
     model   vdw
     2.174 3.080
  nonbonded pdb=" O1P FAD A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   HOH A 601 "
            pdb=" O   HOH A 633 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   HOH A 606 "
            pdb=" O   HOH A 661 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   HOH A 612 "
            pdb=" O   HOH A 620 "
     model   vdw
     2.257 3.040
  ... (remaining 30585 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.020
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.030
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:5.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.005   0.106   3520  Z= 0.189
  Angle     :  0.596   7.222   4801  Z= 0.275
  Chirality :  0.040   0.141    501
  Planarity :  0.004   0.043    576
  Dihedral  : 18.307  88.618   1262
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 19.02 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.44), residues: 397
  helix:  0.95 (0.37), residues: 198
  sheet:  0.34 (0.54), residues: 89
  loop :  0.13 (0.68), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.009   0.001   PHE A  82 
 TRP   0.004   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3518)
  covalent geometry    : angle       0.59637 ( 4801)
  hydrogen bonds       : bond        0.13302 (  187)
  hydrogen bonds       : angle       6.85087 (  540)
  Misc. bond           : bond        0.08250 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  186 TYR cc_start: 0.8912 (m-80) cc_final: 0.8572 (m-80)
REVERT: A  385 LYS cc_start: 0.6845 (tttt) cc_final: 0.6543 (ttmp)
  outliers start: 3
  outliers final: 3
  residues processed: 47
  average time/residue: 0.3391
  time to fit residues: 16.5901
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 SER
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  328 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   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 121 GLN
A 149 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.124857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.103514 restraints weight = 3429.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.28
r_work: 0.3074 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.0786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.222   3520  Z= 0.128
  Angle     :  0.622  14.055   4801  Z= 0.270
  Chirality :  0.040   0.143    501
  Planarity :  0.003   0.041    576
  Dihedral  : 10.313  78.180    504
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.29 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.44), residues: 397
  helix:  2.08 (0.37), residues: 201
  sheet:  0.22 (0.54), residues: 88
  loop :  0.34 (0.67), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 304 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.009   0.001   PHE A 218 
 TRP   0.009   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3518)
  covalent geometry    : angle       0.62241 ( 4801)
  hydrogen bonds       : bond        0.03828 (  187)
  hydrogen bonds       : angle       4.64791 (  540)
  Misc. bond           : bond        0.18167 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  186 TYR cc_start: 0.8783 (m-80) cc_final: 0.8447 (m-80)
REVERT: A  272 ASP cc_start: 0.8771 (p0) cc_final: 0.8499 (p0)
REVERT: A  385 LYS cc_start: 0.6817 (tttt) cc_final: 0.6419 (ttmp)
  outliers start: 7
  outliers final: 1
  residues processed: 53
  average time/residue: 0.3670
  time to fit residues: 20.2815
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   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 = 0.3434 r_free = 0.3434 target = 0.125183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.104039 restraints weight = 3394.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.26
r_work: 0.3083 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.186   3520  Z= 0.120
  Angle     :  0.597  13.677   4801  Z= 0.261
  Chirality :  0.040   0.141    501
  Planarity :  0.003   0.040    576
  Dihedral  : 10.020  82.907    499
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.44 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.43), residues: 397
  helix:  2.09 (0.36), residues: 201
  sheet:  0.20 (0.54), residues: 88
  loop :  0.16 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  51 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.011   0.001   PHE A  82 
 TRP   0.007   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3518)
  covalent geometry    : angle       0.59690 ( 4801)
  hydrogen bonds       : bond        0.03554 (  187)
  hydrogen bonds       : angle       4.50660 (  540)
  Misc. bond           : bond        0.15449 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: A  186 TYR cc_start: 0.8775 (m-80) cc_final: 0.8420 (m-80)
REVERT: A  272 ASP cc_start: 0.8773 (p0) cc_final: 0.8511 (p0)
  outliers start: 5
  outliers final: 1
  residues processed: 49
  average time/residue: 0.3647
  time to fit residues: 18.6745
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.126387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103982 restraints weight = 3354.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.47
r_work: 0.3090 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.159   3520  Z= 0.109
  Angle     :  0.573  12.872   4801  Z= 0.250
  Chirality :  0.039   0.138    501
  Planarity :  0.003   0.039    576
  Dihedral  :  9.623  86.415    499
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.87 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.43), residues: 397
  helix:  2.09 (0.36), residues: 202
  sheet:  0.15 (0.54), residues: 88
  loop :  0.25 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  51 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.009   0.001   PHE A  85 
 TRP   0.007   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3518)
  covalent geometry    : angle       0.57279 ( 4801)
  hydrogen bonds       : bond        0.03289 (  187)
  hydrogen bonds       : angle       4.38838 (  540)
  Misc. bond           : bond        0.13424 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: A  186 TYR cc_start: 0.8682 (m-80) cc_final: 0.8324 (m-80)
REVERT: A  272 ASP cc_start: 0.8743 (p0) cc_final: 0.8463 (p0)
REVERT: A  285 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7704 (tp30)
  outliers start: 9
  outliers final: 1
  residues processed: 53
  average time/residue: 0.4068
  time to fit residues: 22.4258
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.123774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.101116 restraints weight = 3396.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.48
r_work: 0.3050 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.193   3520  Z= 0.149
  Angle     :  0.629  13.908   4801  Z= 0.276
  Chirality :  0.041   0.141    501
  Planarity :  0.003   0.040    576
  Dihedral  : 10.367  83.810    499
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 20.17 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.42), residues: 397
  helix:  1.94 (0.36), residues: 202
  sheet:  0.11 (0.54), residues: 88
  loop :  0.11 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.015   0.002   TYR A 275 
 PHE   0.010   0.001   PHE A  82 
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3518)
  covalent geometry    : angle       0.62862 ( 4801)
  hydrogen bonds       : bond        0.03909 (  187)
  hydrogen bonds       : angle       4.59483 (  540)
  Misc. bond           : bond        0.15800 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7485 (mp)
REVERT: A  272 ASP cc_start: 0.8774 (p0) cc_final: 0.8527 (p0)
REVERT: A  285 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7695 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 47
  average time/residue: 0.4443
  time to fit residues: 21.6256
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0060
   chunk 15 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.125501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102951 restraints weight = 3357.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.47
r_work: 0.3075 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.173   3520  Z= 0.117
  Angle     :  0.585  13.017   4801  Z= 0.256
  Chirality :  0.040   0.138    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.674  80.754    499
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.31 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.43), residues: 397
  helix:  2.02 (0.36), residues: 202
  sheet:  0.12 (0.54), residues: 88
  loop :  0.16 (0.62), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  51 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.009   0.001   PHE A  85 
 TRP   0.006   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3518)
  covalent geometry    : angle       0.58453 ( 4801)
  hydrogen bonds       : bond        0.03418 (  187)
  hydrogen bonds       : angle       4.44225 (  540)
  Misc. bond           : bond        0.14370 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7536 (mp)
REVERT: A  186 TYR cc_start: 0.8690 (m-80) cc_final: 0.8316 (m-80)
REVERT: A  272 ASP cc_start: 0.8748 (p0) cc_final: 0.8485 (p0)
REVERT: A  285 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7678 (tp30)
  outliers start: 5
  outliers final: 1
  residues processed: 50
  average time/residue: 0.3438
  time to fit residues: 17.8771
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3445 r_free = 0.3445 target = 0.124812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.102149 restraints weight = 3451.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.49
r_work: 0.3066 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.181   3520  Z= 0.128
  Angle     :  0.605  13.724   4801  Z= 0.264
  Chirality :  0.040   0.139    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.894  79.245    499
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.60 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.43), residues: 397
  helix:  1.77 (0.36), residues: 208
  sheet:  0.14 (0.54), residues: 88
  loop :  0.31 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  51 
 TYR   0.014   0.002   TYR A 275 
 PHE   0.010   0.001   PHE A  85 
 TRP   0.006   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3518)
  covalent geometry    : angle       0.60519 ( 4801)
  hydrogen bonds       : bond        0.03593 (  187)
  hydrogen bonds       : angle       4.48667 (  540)
  Misc. bond           : bond        0.15190 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7517 (mp)
REVERT: A  186 TYR cc_start: 0.8699 (m-80) cc_final: 0.8323 (m-80)
REVERT: A  272 ASP cc_start: 0.8756 (p0) cc_final: 0.8490 (p0)
REVERT: A  285 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7667 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 51
  average time/residue: 0.4135
  time to fit residues: 21.8386
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  375 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0010
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0470
   chunk 2 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 17 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.2884

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.128438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.106108 restraints weight = 3429.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.49
r_work: 0.3120 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   3520  Z= 0.093
  Angle     :  0.546  11.681   4801  Z= 0.239
  Chirality :  0.038   0.137    501
  Planarity :  0.003   0.039    576
  Dihedral  :  9.044  82.370    499
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.60 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.43), residues: 397
  helix:  2.22 (0.36), residues: 202
  sheet:  0.16 (0.55), residues: 88
  loop :  0.17 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 320 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.009   0.001   PHE A  85 
 TRP   0.006   0.001   TRP A  25 
 HIS   0.005   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3518)
  covalent geometry    : angle       0.54609 ( 4801)
  hydrogen bonds       : bond        0.02880 (  187)
  hydrogen bonds       : angle       4.23072 (  540)
  Misc. bond           : bond        0.10972 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7540 (mp)
REVERT: A  149 ASN cc_start: 0.7877 (m-40) cc_final: 0.6998 (t0)
REVERT: A  264 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7393 (mp10)
REVERT: A  272 ASP cc_start: 0.8717 (p0) cc_final: 0.8497 (p0)
REVERT: A  285 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7691 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 51
  average time/residue: 0.3968
  time to fit residues: 20.9639
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.125657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.103251 restraints weight = 3395.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.48
r_work: 0.3083 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.170   3520  Z= 0.120
  Angle     :  0.594  13.397   4801  Z= 0.259
  Chirality :  0.040   0.138    501
  Planarity :  0.003   0.039    576
  Dihedral  :  9.568  78.657    499
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 20.46 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.43), residues: 397
  helix:  1.90 (0.36), residues: 208
  sheet:  0.13 (0.54), residues: 88
  loop :  0.38 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  51 
 TYR   0.015   0.001   TYR A 275 
 PHE   0.010   0.001   PHE A  85 
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3518)
  covalent geometry    : angle       0.59387 ( 4801)
  hydrogen bonds       : bond        0.03447 (  187)
  hydrogen bonds       : angle       4.40121 (  540)
  Misc. bond           : bond        0.13697 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7506 (mp)
REVERT: A  186 TYR cc_start: 0.8630 (m-80) cc_final: 0.8238 (m-80)
REVERT: A  272 ASP cc_start: 0.8750 (p0) cc_final: 0.8473 (p0)
REVERT: A  285 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7676 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 51
  average time/residue: 0.4139
  time to fit residues: 21.9581
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0770
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.8940

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.124538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.101961 restraints weight = 3446.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.49
r_work: 0.3066 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.185   3520  Z= 0.137
  Angle     :  0.616  14.062   4801  Z= 0.270
  Chirality :  0.041   0.139    501
  Planarity :  0.003   0.040    576
  Dihedral  :  9.989  78.144    499
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 20.17 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.43), residues: 397
  helix:  1.79 (0.36), residues: 208
  sheet:  0.13 (0.54), residues: 88
  loop :  0.30 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.015   0.002   TYR A 275 
 PHE   0.011   0.001   PHE A  85 
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3518)
  covalent geometry    : angle       0.61554 ( 4801)
  hydrogen bonds       : bond        0.03733 (  187)
  hydrogen bonds       : angle       4.52799 (  540)
  Misc. bond           : bond        0.14784 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7413 (mp)
REVERT: A  186 TYR cc_start: 0.8632 (m-80) cc_final: 0.8197 (m-80)
REVERT: A  272 ASP cc_start: 0.8763 (p0) cc_final: 0.8477 (p0)
REVERT: A  285 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7659 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 50
  average time/residue: 0.4507
  time to fit residues: 23.3863
Evaluate side-chains
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.124724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.101972 restraints weight = 3411.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.50
r_work: 0.3062 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.184   3520  Z= 0.140
  Angle     :  0.627  13.941   4801  Z= 0.276
  Chirality :  0.041   0.139    501
  Planarity :  0.003   0.040    576
  Dihedral  : 10.105  78.280    499
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 20.75 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.42), residues: 397
  helix:  1.74 (0.36), residues: 208
  sheet:  0.09 (0.54), residues: 88
  loop :  0.27 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.015   0.002   TYR A 275 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.005   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3518)
  covalent geometry    : angle       0.62718 ( 4801)
  hydrogen bonds       : bond        0.03772 (  187)
  hydrogen bonds       : angle       4.54948 (  540)
  Misc. bond           : bond        0.14760 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1316.79 seconds
wall clock time: 23 minutes 9.76 seconds (1389.76 seconds total)