Starting phenix.real_space_refine
on Tue Feb  3 19:13:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qqm_53308/02_2026/9qqm_53308.map"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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
     S      19      5.16       5
     C    2096      2.51       5
     N     495      2.21       5
     O     522      1.98       5
     H    3129      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6261
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 6261
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 15, 'TRANS': 377}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.81, per 1000 atoms: 0.13
  Number of scatterers: 6261
  At special positions: 0
  Unit cell: (77.4, 62.565, 71.595, 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      19     16.00
     O     522      8.00
     N     495      7.00
     C    2096      6.00
     H    3129      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 462 " - pdb=" SG  CYS A 465 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 176.3 milliseconds
  

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  728

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      84.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 56
      removed outlier: 4.059A  pdb=" N   SER A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 63
      removed outlier: 4.055A  pdb=" N   VAL A  61 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LEU A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 73
    Processing helix  chain 'A' and resid 73 through 109
      removed outlier: 3.703A  pdb=" N   GLU A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 128
    Processing helix  chain 'A' and resid 129 through 163
      removed outlier: 3.823A  pdb=" N   TYR A 161 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 180
    Processing helix  chain 'A' and resid 181 through 184
    Processing helix  chain 'A' and resid 192 through 217
      removed outlier: 4.045A  pdb=" N   PHE A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   THR A 205 " --> pdb=" O   MET A 201 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 211 " --> pdb=" O   TRP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 244
    Processing helix  chain 'A' and resid 265 through 290
      removed outlier: 4.321A  pdb=" N   ALA A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   THR A 271 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 306 through 340
      removed outlier: 3.959A  pdb=" N   THR A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      Proline residue:  A 330  - end of helix
    Processing helix  chain 'A' and resid 350 through 368
      removed outlier: 3.977A  pdb=" N   ARG A 354 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 372 through 387
      removed outlier: 3.802A  pdb=" N   VAL A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   SER A 384 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   PHE A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 399
      removed outlier: 3.763A  pdb=" N   ALA A 392 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 407
    Processing helix  chain 'A' and resid 413 through 416
    Processing helix  chain 'A' and resid 417 through 436
    Processing helix  chain 'A' and resid 439 through 457

    223 hydrogen bonds defined for protein.
    654 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3123
        1.03 -     1.23: 6
        1.23 -     1.42: 1413
        1.42 -     1.62: 1786
        1.62 -     1.81: 30
  Bond restraints: 6358
  Sorted by residual:
  bond pdb=" CG  PRO A  66 "
       pdb=" CD  PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.503  1.485  0.018 3.40e-02 8.65e+02 2.71e-01
  bond pdb=" CG  PRO A 330 "
       pdb=" CD  PRO A 330 "
    ideal  model  delta    sigma   weight residual
    1.503  1.486  0.017 3.40e-02 8.65e+02 2.47e-01
  bond pdb=" CG  LYS A 223 "
       pdb=" CD  LYS A 223 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 3.00e-02 1.11e+03 2.46e-01
  bond pdb=" CB  THR A 172 "
       pdb=" CG2 THR A 172 "
    ideal  model  delta    sigma   weight residual
    1.521  1.506  0.015 3.30e-02 9.18e+02 2.10e-01
  bond pdb=" N   TYR A  84 "
       pdb=" CA  TYR A  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.453  0.006 1.28e-02 6.10e+03 2.03e-01
  ... (remaining 6353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.09: 11431
        7.09 -    14.18: 0
       14.18 -    21.27: 0
       21.27 -    28.35: 2
       28.35 -    35.44: 13
  Bond angle restraints: 11446
  Sorted by residual:
  angle pdb=" C   ALA A 248 "
        pdb=" CA  ALA A 248 "
        pdb=" HA  ALA A 248 "
      ideal   model   delta    sigma   weight residual
     109.00   73.56   35.44 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" C   THR A 250 "
        pdb=" CA  THR A 250 "
        pdb=" HA  THR A 250 "
      ideal   model   delta    sigma   weight residual
     109.00   73.76   35.24 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" C   GLU A 107 "
        pdb=" CA  GLU A 107 "
        pdb=" HA  GLU A 107 "
      ideal   model   delta    sigma   weight residual
     109.00   74.31   34.69 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" N   THR A 250 "
        pdb=" CA  THR A 250 "
        pdb=" HA  THR A 250 "
      ideal   model   delta    sigma   weight residual
     110.00   75.69   34.31 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" N   GLU A 107 "
        pdb=" CA  GLU A 107 "
        pdb=" HA  GLU A 107 "
      ideal   model   delta    sigma   weight residual
     110.00   75.71   34.29 3.00e+00 1.11e-01 1.31e+02
  ... (remaining 11441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 2602
       15.96 -    31.91: 274
       31.91 -    47.87: 80
       47.87 -    63.82: 50
       63.82 -    79.78: 9
  Dihedral angle restraints: 3015
    sinusoidal: 1541
      harmonic: 1474
  Sorted by residual:
  dihedral pdb=" C   THR A 250 "
           pdb=" N   THR A 250 "
           pdb=" CA  THR A 250 "
           pdb=" CB  THR A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.90    9.90     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" C   GLU A 107 "
           pdb=" N   GLU A 107 "
           pdb=" CA  GLU A 107 "
           pdb=" CB  GLU A 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.93    9.33     0      2.50e+00 1.60e-01 1.39e+01
  dihedral pdb=" C   ALA A 248 "
           pdb=" N   ALA A 248 "
           pdb=" CA  ALA A 248 "
           pdb=" CB  ALA A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.79    9.19     0      2.50e+00 1.60e-01 1.35e+01
  ... (remaining 3012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 479
       0.079 -    0.158: 21
       0.158 -    0.237: 0
       0.237 -    0.316: 0
       0.316 -    0.395: 3
  Chirality restraints: 503
  Sorted by residual:
  chirality pdb=" CA  THR A 250 "
            pdb=" N   THR A 250 "
            pdb=" C   THR A 250 "
            pdb=" CB  THR A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CA  GLU A 107 "
            pdb=" N   GLU A 107 "
            pdb=" C   GLU A 107 "
            pdb=" CB  GLU A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CA  ALA A 248 "
            pdb=" N   ALA A 248 "
            pdb=" C   ALA A 248 "
            pdb=" CB  ALA A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.15    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 500 not shown)

  Planarity restraints: 900
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 372 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A 373 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 359 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.92e+00
        pdb=" N   PRO A 360 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 360 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 360 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "   -0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A  66 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 897 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 439
        2.21 -     2.81: 12999
        2.81 -     3.41: 17881
        3.41 -     4.00: 22954
        4.00 -     4.60: 35592
  Nonbonded interactions: 89865
  Sorted by model distance:
  nonbonded pdb=" HA  GLU A 107 "
            pdb=" HB2 GLU A 107 "
     model   vdw
     1.614 1.952
  nonbonded pdb=" HA  ALA A 248 "
            pdb=" HB1 ALA A 248 "
     model   vdw
     1.637 1.952
  nonbonded pdb=" H   THR A 250 "
            pdb=" HA  THR A 250 "
     model   vdw
     1.680 1.816
  nonbonded pdb="HG13 ILE A 253 "
            pdb="HD12 ILE A 253 "
     model   vdw
     1.720 1.952
  nonbonded pdb=" H   GLU A 107 "
            pdb=" HA  GLU A 107 "
     model   vdw
     1.730 1.816
  ... (remaining 89860 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:             4.160
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.710
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
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      :  0.002   0.019   3230  Z= 0.086
  Angle     :  0.420   4.788   4405  Z= 0.223
  Chirality :  0.044   0.395    503
  Planarity :  0.003   0.037    528
  Dihedral  : 16.612  79.776   1083
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 20.48 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.73 (0.45), residues: 383
  helix:  2.10 (0.32), residues: 293
  sheet:  None (None), residues: 0
  loop :  1.01 (0.73), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 169 
 TYR   0.007   0.001   TYR A 161 
 PHE   0.009   0.001   PHE A 244 
 TRP   0.003   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A 342 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 3229)
  covalent geometry    : angle       0.42013 ( 4403)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.27387 (    2)
  hydrogen bonds       : bond        0.16145 (  223)
  hydrogen bonds       : angle       6.06007 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8365 (t80)
REVERT: A   75 MET cc_start: 0.6888 (mtt) cc_final: 0.6602 (ttp)
REVERT: A  254 MET cc_start: 0.3961 (ptp) cc_final: 0.3730 (ptp)
  outliers start: 2
  outliers final: 1
  residues processed: 50
  average time/residue: 0.0910
  time to fit residues: 5.9540
Evaluate side-chains
  50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.158454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.136374 restraints weight = 10873.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.53
r_work: 0.3384 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3230  Z= 0.158
  Angle     :  0.501   4.759   4405  Z= 0.278
  Chirality :  0.047   0.397    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.703  55.236    425
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 20.78 %
    Favored  : 77.71 %
  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 are not related in a simple way.
  whole:  2.47 (0.45), residues: 383
  helix:  2.02 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.30 (0.78), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.015   0.001   TYR A 204 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 171 
 HIS   0.002   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3229)
  covalent geometry    : angle       0.50098 ( 4403)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.39220 (    2)
  hydrogen bonds       : bond        0.04705 (  223)
  hydrogen bonds       : angle       4.74484 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8322 (t80)
REVERT: A   75 MET cc_start: 0.7042 (mtt) cc_final: 0.6648 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0772
  time to fit residues: 5.2904
Evaluate side-chains
  51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  404 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 35 optimal weight:    0.2980
   chunk 3 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0970
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.2756

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.162608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.141064 restraints weight = 10624.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.50
r_work: 0.3499 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.0722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3230  Z= 0.102
  Angle     :  0.450   4.768   4405  Z= 0.246
  Chirality :  0.045   0.399    503
  Planarity :  0.004   0.035    528
  Dihedral  :  4.527  55.015    423
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.69 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  2.70 (0.45), residues: 383
  helix:  2.23 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.18 (0.75), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.007   0.001   PHE A 175 
 TRP   0.005   0.001   TRP A 207 
 HIS   0.002   0.000   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 3229)
  covalent geometry    : angle       0.44968 ( 4403)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.21246 (    2)
  hydrogen bonds       : bond        0.04153 (  223)
  hydrogen bonds       : angle       4.52840 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8263 (t80)
REVERT: A   75 MET cc_start: 0.6934 (mtt) cc_final: 0.6616 (ttp)
  outliers start: 5
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0956
  time to fit residues: 6.7818
Evaluate side-chains
  52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.158614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.136558 restraints weight = 10793.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.52
r_work: 0.3354 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.0949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3230  Z= 0.154
  Angle     :  0.480   4.723   4405  Z= 0.263
  Chirality :  0.046   0.400    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.629  53.699    423
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.69 %
    Favored  : 76.51 %
  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 are not related in a simple way.
  whole:  2.51 (0.45), residues: 383
  helix:  2.08 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.18 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.014   0.001   TYR A 161 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.006   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3229)
  covalent geometry    : angle       0.48036 ( 4403)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.45487 (    2)
  hydrogen bonds       : bond        0.04142 (  223)
  hydrogen bonds       : angle       4.56646 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8297 (t80)
REVERT: A   75 MET cc_start: 0.7063 (mtt) cc_final: 0.6670 (ttp)
  outliers start: 6
  outliers final: 4
  residues processed: 54
  average time/residue: 0.0937
  time to fit residues: 6.6598
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.159939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.137647 restraints weight = 10857.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.55
r_work: 0.3342 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3230  Z= 0.140
  Angle     :  0.474   4.690   4405  Z= 0.260
  Chirality :  0.046   0.399    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.657  53.844    423
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.99 %
    Favored  : 76.20 %
  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 are not related in a simple way.
  whole:  2.46 (0.45), residues: 383
  helix:  2.05 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.17 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.012   0.001   TYR A 161 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 207 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3229)
  covalent geometry    : angle       0.47391 ( 4403)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.37971 (    2)
  hydrogen bonds       : bond        0.04036 (  223)
  hydrogen bonds       : angle       4.51882 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8280 (t80)
REVERT: A   75 MET cc_start: 0.7161 (mtt) cc_final: 0.6676 (ttp)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1175
  time to fit residues: 8.4708
Evaluate side-chains
  55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.157750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.135338 restraints weight = 10707.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.54
r_work: 0.3419 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3230  Z= 0.159
  Angle     :  0.488   4.650   4405  Z= 0.268
  Chirality :  0.047   0.397    503
  Planarity :  0.004   0.039    528
  Dihedral  :  4.740  53.457    423
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.78 %
    Favored  : 77.11 %
  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 are not related in a simple way.
  whole:  2.37 (0.45), residues: 383
  helix:  1.98 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.17 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.015   0.001   TYR A 161 
 PHE   0.012   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 287 
 HIS   0.002   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3229)
  covalent geometry    : angle       0.48815 ( 4403)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.45968 (    2)
  hydrogen bonds       : bond        0.04151 (  223)
  hydrogen bonds       : angle       4.53133 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8260 (t80)
REVERT: A   75 MET cc_start: 0.7194 (mtt) cc_final: 0.6694 (ttp)
  outliers start: 7
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1026
  time to fit residues: 7.5287
Evaluate side-chains
  55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0980
   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 = 0.3748 r_free = 0.3748 target = 0.159102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.136648 restraints weight = 10624.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.54
r_work: 0.3453 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3230  Z= 0.122
  Angle     :  0.473   4.690   4405  Z= 0.260
  Chirality :  0.046   0.399    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.683  54.006    423
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.99 %
    Favored  : 76.51 %
  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 are not related in a simple way.
  whole:  2.47 (0.45), residues: 383
  helix:  2.05 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.19 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.012   0.001   TYR A 161 
 PHE   0.009   0.001   PHE A 196 
 TRP   0.005   0.001   TRP A 207 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3229)
  covalent geometry    : angle       0.47298 ( 4403)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.36127 (    2)
  hydrogen bonds       : bond        0.03910 (  223)
  hydrogen bonds       : angle       4.46986 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8249 (t80)
REVERT: A   75 MET cc_start: 0.7126 (mtt) cc_final: 0.6663 (ttp)
REVERT: A  362 TRP cc_start: 0.7905 (t60) cc_final: 0.7605 (t60)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 0.0988
  time to fit residues: 6.8644
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.160285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.137838 restraints weight = 10728.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.55
r_work: 0.3397 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3230  Z= 0.119
  Angle     :  0.467   4.700   4405  Z= 0.255
  Chirality :  0.046   0.397    503
  Planarity :  0.004   0.039    528
  Dihedral  :  4.660  53.800    423
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.99 %
    Favored  : 76.20 %
  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 are not related in a simple way.
  whole:  2.54 (0.45), residues: 383
  helix:  2.09 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.24 (0.77), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 405 
 TYR   0.012   0.001   TYR A 161 
 PHE   0.009   0.001   PHE A 244 
 TRP   0.004   0.001   TRP A 171 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3229)
  covalent geometry    : angle       0.46746 ( 4403)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.36645 (    2)
  hydrogen bonds       : bond        0.03812 (  223)
  hydrogen bonds       : angle       4.44707 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8234 (t80)
REVERT: A   75 MET cc_start: 0.7157 (mtt) cc_final: 0.6657 (ttp)
REVERT: A  362 TRP cc_start: 0.7881 (t60) cc_final: 0.7594 (t60)
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0878
  time to fit residues: 6.2732
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0040
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.2992

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.162277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.139922 restraints weight = 10693.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.55
r_work: 0.3481 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3230  Z= 0.099
  Angle     :  0.455   4.732   4405  Z= 0.246
  Chirality :  0.045   0.397    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.609  54.152    423
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.69 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  2.58 (0.45), residues: 383
  helix:  2.14 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  0.20 (0.75), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.009   0.001   PHE A 196 
 TRP   0.004   0.001   TRP A 207 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 3229)
  covalent geometry    : angle       0.45461 ( 4403)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.29696 (    2)
  hydrogen bonds       : bond        0.03593 (  223)
  hydrogen bonds       : angle       4.39325 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8215 (t80)
REVERT: A   75 MET cc_start: 0.7018 (mtt) cc_final: 0.6652 (ttp)
REVERT: A  362 TRP cc_start: 0.7822 (t60) cc_final: 0.7542 (t60)
  outliers start: 5
  outliers final: 2
  residues processed: 52
  average time/residue: 0.0985
  time to fit residues: 6.8030
Evaluate side-chains
  52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    0.2980
   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 = 0.3738 r_free = 0.3738 target = 0.158157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.135829 restraints weight = 10791.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.52
r_work: 0.3481 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3230  Z= 0.139
  Angle     :  0.479   4.704   4405  Z= 0.262
  Chirality :  0.046   0.397    503
  Planarity :  0.004   0.038    528
  Dihedral  :  4.662  53.307    423
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 21.39 %
    Favored  : 77.11 %
  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 are not related in a simple way.
  whole:  2.52 (0.45), residues: 383
  helix:  2.08 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.19 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.013   0.001   TYR A 161 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 287 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3229)
  covalent geometry    : angle       0.47941 ( 4403)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.42224 (    2)
  hydrogen bonds       : bond        0.03832 (  223)
  hydrogen bonds       : angle       4.48326 (  654)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  249 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   69 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8259 (t80)
REVERT: A   75 MET cc_start: 0.7073 (mtt) cc_final: 0.6707 (ttp)
REVERT: A  362 TRP cc_start: 0.7879 (t60) cc_final: 0.7605 (t60)
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0877
  time to fit residues: 5.8903
Evaluate side-chains
  53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue   69 PHE
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  454 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.158222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.135284 restraints weight = 10740.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.57
r_work: 0.3370 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3230  Z= 0.144
  Angle     :  0.483   4.680   4405  Z= 0.265
  Chirality :  0.046   0.397    503
  Planarity :  0.004   0.039    528
  Dihedral  :  4.703  53.616    423
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 21.99 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  2.43 (0.45), residues: 383
  helix:  2.02 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop :  0.14 (0.76), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.013   0.001   TYR A 161 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 171 
 HIS   0.001   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3229)
  covalent geometry    : angle       0.48330 ( 4403)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.40277 (    2)
  hydrogen bonds       : bond        0.03911 (  223)
  hydrogen bonds       : angle       4.49309 (  654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2070.81 seconds
wall clock time: 35 minutes 46.65 seconds (2146.65 seconds total)