Starting phenix.real_space_refine
on Fri May  9 20:08:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jjl_36360/05_2025/8jjl_36360_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    1986      2.51       5
     N     488      2.21       5
     O     532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3026
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2998
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 8, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DZQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.55, per 1000 atoms: 0.84
  Number of scatterers: 3026
  At special positions: 0
  Unit cell: (55.76, 96.76, 92.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     532      8.00
     N     488      7.00
     C    1986      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 190 " 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: 0.83
  Conformation dependent library (CDL) restraints added in 579.6 milliseconds
  

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 0 sheets defined
      89.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 61
      removed outlier: 3.542A  pdb=" N   VAL A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 96
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 102 through 133
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 3.665A  pdb=" N   SER A 143 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 171
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 3.618A  pdb=" N   ILE A 182 " --> pdb=" O   HIS A 178 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 208
      removed outlier: 4.571A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 249
      removed outlier: 3.502A  pdb=" N   THR A 239 " --> pdb=" O   ASP A 235 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 240 " --> pdb=" O   ASN A 236 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 273
      removed outlier: 4.386A  pdb=" N   VAL A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 303
      removed outlier: 3.761A  pdb=" N   PHE A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP A 289 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 314
      removed outlier: 3.689A  pdb=" N   ALA A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 366
      removed outlier: 3.934A  pdb=" N   THR A 319 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 327 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
      Proline residue:  A 355  - end of helix
      removed outlier: 4.067A  pdb=" N   GLN A 366 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 385
    Processing helix  chain 'A' and resid 387 through 394
      removed outlier: 4.022A  pdb=" N   LEU A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 407

    244 hydrogen bonds defined for protein.
    732 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: 0.81

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 478
        1.31 -     1.44: 851
        1.44 -     1.56: 1735
        1.56 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3095
  Sorted by residual:
  bond pdb=" C21 DZQ A 501 "
       pdb=" O22 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.362  1.455 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" C   TYR A 328 "
       pdb=" O   TYR A 328 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.16e-02 7.43e+03 1.86e+01
  bond pdb=" C   ILE A 325 "
       pdb=" O   ILE A 325 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.19e-02 7.06e+03 1.34e+01
  bond pdb=" C24 DZQ A 501 "
       pdb=" N26 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.354  1.415 -0.061 2.00e-02 2.50e+03 9.21e+00
  bond pdb=" C20 DZQ A 501 "
       pdb=" N26 DZQ A 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.447 -0.053 2.00e-02 2.50e+03 6.89e+00
  ... (remaining 3090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 4014
        1.63 -     3.26: 147
        3.26 -     4.88: 32
        4.88 -     6.51: 8
        6.51 -     8.14: 4
  Bond angle restraints: 4205
  Sorted by residual:
  angle pdb=" N   ILE A 325 "
        pdb=" CA  ILE A 325 "
        pdb=" C   ILE A 325 "
      ideal   model   delta    sigma   weight residual
     110.72  102.58    8.14 1.01e+00 9.80e-01 6.49e+01
  angle pdb=" N   LEU A 329 "
        pdb=" CA  LEU A 329 "
        pdb=" C   LEU A 329 "
      ideal   model   delta    sigma   weight residual
     111.11  104.67    6.44 1.20e+00 6.94e-01 2.88e+01
  angle pdb=" O   ALA A 323 "
        pdb=" C   ALA A 323 "
        pdb=" N   TYR A 324 "
      ideal   model   delta    sigma   weight residual
     122.33  129.34   -7.01 1.34e+00 5.57e-01 2.74e+01
  angle pdb=" CA  ALA A 323 "
        pdb=" C   ALA A 323 "
        pdb=" N   TYR A 324 "
      ideal   model   delta    sigma   weight residual
     117.82  110.85    6.97 1.42e+00 4.96e-01 2.41e+01
  angle pdb=" N   LYS A 334 "
        pdb=" CA  LYS A 334 "
        pdb=" C   LYS A 334 "
      ideal   model   delta    sigma   weight residual
     111.82  107.63    4.19 1.16e+00 7.43e-01 1.30e+01
  ... (remaining 4200 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 1605
       15.88 -    31.76: 181
       31.76 -    47.64: 37
       47.64 -    63.52: 8
       63.52 -    79.40: 5
  Dihedral angle restraints: 1836
    sinusoidal: 728
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CA  HIS A 178 "
           pdb=" C   HIS A 178 "
           pdb=" N   GLN A 179 "
           pdb=" CA  GLN A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.84  -21.16     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C   TYR A 324 "
           pdb=" N   TYR A 324 "
           pdb=" CA  TYR A 324 "
           pdb=" CB  TYR A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.22   -9.38     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CA  ASP A 367 "
           pdb=" C   ASP A 367 "
           pdb=" N   ASN A 368 "
           pdb=" CA  ASN A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 400
       0.055 -    0.110: 77
       0.110 -    0.165: 7
       0.165 -    0.220: 3
       0.220 -    0.275: 1
  Chirality restraints: 488
  Sorted by residual:
  chirality pdb=" CA  TYR A 324 "
            pdb=" N   TYR A 324 "
            pdb=" C   TYR A 324 "
            pdb=" CB  TYR A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  LEU A 233 "
            pdb=" N   LEU A 233 "
            pdb=" C   LEU A 233 "
            pdb=" CB  LEU A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE A 325 "
            pdb=" CA  ILE A 325 "
            pdb=" CG1 ILE A 325 "
            pdb=" CG2 ILE A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.45e-01
  ... (remaining 485 not shown)

  Planarity restraints: 515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 323 "   -0.023 2.00e-02 2.50e+03   5.18e-02 2.68e+01
        pdb=" C   ALA A 323 "    0.089 2.00e-02 2.50e+03
        pdb=" O   ALA A 323 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   TYR A 324 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 227 "    0.022 2.00e-02 2.50e+03   4.40e-02 1.93e+01
        pdb=" C   LYS A 227 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LYS A 227 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ARG A 228 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 206 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   VAL A 206 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 206 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER A 207 "    0.015 2.00e-02 2.50e+03
  ... (remaining 512 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 102
        2.72 -     3.26: 3413
        3.26 -     3.81: 5334
        3.81 -     4.35: 6239
        4.35 -     4.90: 10361
  Nonbonded interactions: 25449
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 113 "
            pdb=" OH  TYR A 383 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OH  TYR A 219 "
            pdb=" O   LEU A 339 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" NZ  LYS A 257 "
            pdb=" OD1 ASN A 303 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   PHE A 139 "
            pdb=" OG  SER A 143 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG1 THR A 118 "
            pdb=" OG  SER A 207 "
     model   vdw
     2.338 3.040
  ... (remaining 25444 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:                  0.010
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.100
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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   0.093   3097  Z= 0.285
  Angle     :  0.766   8.138   4209  Z= 0.494
  Chirality :  0.045   0.275    488
  Planarity :  0.005   0.052    515
  Dihedral  : 14.230  79.405   1108
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  0.93 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.46), residues: 371
  helix:  1.35 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.68 (0.85), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 380 
 HIS   0.005   0.001   HIS A 178 
 PHE   0.008   0.001   PHE A 357 
 TYR   0.031   0.002   TYR A 328 
 ARG   0.001   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17535 (  244)
  hydrogen bonds       : angle       5.98802 (  732)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.49006 (    4)
  covalent geometry    : bond        0.00469 ( 3095)
  covalent geometry    : angle       0.76650 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.7041 (m-10) cc_final: 0.6517 (m-10)
REVERT: A   82 MET cc_start: 0.7587 (tmm) cc_final: 0.6999 (ttp)
REVERT: A  151 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5952 (tpm170)
  outliers start: 5
  outliers final: 3
  residues processed: 101
  average time/residue: 0.1418
  time to fit residues: 17.2358
Evaluate side-chains
  75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  327 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0020
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 311 GLN
A 363 HIS
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.150714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.119442 restraints weight = 4278.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.47
r_work: 0.3435 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3097  Z= 0.145
  Angle     :  0.572   6.578   4209  Z= 0.306
  Chirality :  0.039   0.113    488
  Planarity :  0.004   0.043    515
  Dihedral  :  6.322  44.466    430
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.07 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.44), residues: 371
  helix:  1.11 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.08 (1.02), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A  71 
 TYR   0.018   0.002   TYR A 328 
 ARG   0.002   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04902 (  244)
  hydrogen bonds       : angle       4.47405 (  732)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.99626 (    4)
  covalent geometry    : bond        0.00302 ( 3095)
  covalent geometry    : angle       0.57118 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7326 (m-10) cc_final: 0.6247 (m-10)
REVERT: A   82 MET cc_start: 0.7917 (tmm) cc_final: 0.7188 (ttp)
REVERT: A  135 ILE cc_start: 0.8047 (mm) cc_final: 0.7778 (mm)
REVERT: A  223 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7060 (m-80)
REVERT: A  238 GLU cc_start: 0.8410 (tt0) cc_final: 0.7882 (tp30)
REVERT: A  328 TYR cc_start: 0.6857 (t80) cc_final: 0.6121 (t80)
REVERT: A  332 CYS cc_start: 0.8304 (t) cc_final: 0.7897 (m)
  outliers start: 10
  outliers final: 4
  residues processed: 90
  average time/residue: 0.1309
  time to fit residues: 14.6169
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.149115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.117555 restraints weight = 4221.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.48
r_work: 0.3414 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3097  Z= 0.149
  Angle     :  0.595  11.018   4209  Z= 0.313
  Chirality :  0.040   0.249    488
  Planarity :  0.003   0.034    515
  Dihedral  :  5.387  42.476    422
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 13.93 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.44), residues: 371
  helix:  1.26 (0.28), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.17 (1.02), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.019   0.002   TYR A 328 
 ARG   0.001   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04818 (  244)
  hydrogen bonds       : angle       4.39294 (  732)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       3.30235 (    4)
  covalent geometry    : bond        0.00323 ( 3095)
  covalent geometry    : angle       0.58609 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7996 (tmm) cc_final: 0.7337 (ttp)
REVERT: A  223 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7050 (m-80)
REVERT: A  238 GLU cc_start: 0.8402 (tt0) cc_final: 0.7840 (tp30)
REVERT: A  308 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8682 (mmmt)
REVERT: A  328 TYR cc_start: 0.6932 (t80) cc_final: 0.5961 (t80)
REVERT: A  332 CYS cc_start: 0.8308 (t) cc_final: 0.7683 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1198
  time to fit residues: 12.4124
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.0070
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.149987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.118143 restraints weight = 4298.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.53
r_work: 0.3422 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3097  Z= 0.131
  Angle     :  0.558   8.456   4209  Z= 0.295
  Chirality :  0.038   0.189    488
  Planarity :  0.003   0.028    515
  Dihedral  :  5.284  47.169    422
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.17 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.44), residues: 371
  helix:  1.61 (0.29), residues: 304
  sheet:  None (None), residues: 0
  loop : -0.67 (0.87), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.009   0.001   PHE A 208 
 TYR   0.023   0.002   TYR A 324 
 ARG   0.000   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  244)
  hydrogen bonds       : angle       4.24869 (  732)
  SS BOND              : bond        0.00602 (    2)
  SS BOND              : angle       2.92977 (    4)
  covalent geometry    : bond        0.00270 ( 3095)
  covalent geometry    : angle       0.55122 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8012 (tmm) cc_final: 0.7329 (ttp)
REVERT: A   96 MET cc_start: 0.7491 (mtt) cc_final: 0.6675 (mmm)
REVERT: A  223 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7069 (m-80)
REVERT: A  238 GLU cc_start: 0.8468 (tt0) cc_final: 0.7888 (tp30)
REVERT: A  308 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8716 (mmmt)
REVERT: A  328 TYR cc_start: 0.7194 (t80) cc_final: 0.6258 (t80)
REVERT: A  332 CYS cc_start: 0.8218 (t) cc_final: 0.7744 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 83
  average time/residue: 0.1225
  time to fit residues: 12.6784
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.148973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.116447 restraints weight = 4277.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.60
r_work: 0.3390 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3097  Z= 0.139
  Angle     :  0.558   7.013   4209  Z= 0.293
  Chirality :  0.038   0.163    488
  Planarity :  0.003   0.026    515
  Dihedral  :  5.218  46.786    422
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.34 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.44), residues: 371
  helix:  1.69 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.62 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.032   0.002   TYR A 324 
 ARG   0.000   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04528 (  244)
  hydrogen bonds       : angle       4.20923 (  732)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       2.62685 (    4)
  covalent geometry    : bond        0.00299 ( 3095)
  covalent geometry    : angle       0.55274 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.6866 (ttt) cc_final: 0.6486 (ttt)
REVERT: A   82 MET cc_start: 0.8047 (tmm) cc_final: 0.7399 (ttp)
REVERT: A   96 MET cc_start: 0.7506 (mtt) cc_final: 0.6695 (mmm)
REVERT: A  223 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7110 (m-80)
REVERT: A  238 GLU cc_start: 0.8447 (tt0) cc_final: 0.7876 (tp30)
REVERT: A  308 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8728 (mmmt)
REVERT: A  328 TYR cc_start: 0.7279 (t80) cc_final: 0.6395 (t80)
REVERT: A  332 CYS cc_start: 0.8189 (t) cc_final: 0.7734 (m)
REVERT: A  333 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7446 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1248
  time to fit residues: 12.6258
Evaluate side-chains
  82 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0870
   chunk 5 optimal weight:    0.0770
   chunk 27 optimal weight:    0.0170
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.1954

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.152309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.119859 restraints weight = 4409.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.64
r_work: 0.3431 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3097  Z= 0.119
  Angle     :  0.560   7.903   4209  Z= 0.291
  Chirality :  0.037   0.131    488
  Planarity :  0.003   0.024    515
  Dihedral  :  5.226  49.769    422
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.58 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.44), residues: 371
  helix:  1.74 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.76 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.009   0.001   PHE A 208 
 TYR   0.033   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  244)
  hydrogen bonds       : angle       4.16035 (  732)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       2.29887 (    4)
  covalent geometry    : bond        0.00235 ( 3095)
  covalent geometry    : angle       0.55537 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7981 (tmm) cc_final: 0.7304 (ttp)
REVERT: A   96 MET cc_start: 0.7569 (mtt) cc_final: 0.6751 (mmm)
REVERT: A   99 TRP cc_start: 0.8067 (t-100) cc_final: 0.7690 (t-100)
REVERT: A  223 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7138 (m-80)
REVERT: A  238 GLU cc_start: 0.8409 (tt0) cc_final: 0.7839 (tp30)
REVERT: A  300 LYS cc_start: 0.8823 (tptm) cc_final: 0.7843 (ttpp)
REVERT: A  308 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8715 (mmmt)
REVERT: A  328 TYR cc_start: 0.7357 (t80) cc_final: 0.6470 (t80)
REVERT: A  332 CYS cc_start: 0.8088 (t) cc_final: 0.7757 (m)
  outliers start: 14
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1175
  time to fit residues: 12.0536
Evaluate side-chains
  81 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  379 ASN
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.148456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.117720 restraints weight = 4296.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.40
r_work: 0.3400 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3097  Z= 0.144
  Angle     :  0.568   6.204   4209  Z= 0.295
  Chirality :  0.038   0.140    488
  Planarity :  0.003   0.022    515
  Dihedral  :  5.168  47.463    422
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.27 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.45), residues: 371
  helix:  1.73 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.69 (0.85), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.032   0.002   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  244)
  hydrogen bonds       : angle       4.14275 (  732)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       2.30744 (    4)
  covalent geometry    : bond        0.00314 ( 3095)
  covalent geometry    : angle       0.56401 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.6811 (ttt) cc_final: 0.6527 (ttt)
REVERT: A   82 MET cc_start: 0.8084 (tmm) cc_final: 0.7391 (ttp)
REVERT: A   96 MET cc_start: 0.7527 (mtt) cc_final: 0.6717 (mmm)
REVERT: A   99 TRP cc_start: 0.8173 (t-100) cc_final: 0.7803 (t-100)
REVERT: A  223 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7165 (m-80)
REVERT: A  238 GLU cc_start: 0.8455 (tt0) cc_final: 0.7849 (tp30)
REVERT: A  300 LYS cc_start: 0.8837 (tptm) cc_final: 0.7764 (ttmt)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1221
  time to fit residues: 12.1026
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.116088 restraints weight = 4328.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.60
r_work: 0.3381 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3097  Z= 0.139
  Angle     :  0.583   7.692   4209  Z= 0.299
  Chirality :  0.039   0.132    488
  Planarity :  0.003   0.021    515
  Dihedral  :  5.182  46.276    422
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.20 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.45), residues: 371
  helix:  1.68 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.62 (0.88), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 172 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.034   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  244)
  hydrogen bonds       : angle       4.15741 (  732)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       2.32324 (    4)
  covalent geometry    : bond        0.00303 ( 3095)
  covalent geometry    : angle       0.57915 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.6766 (ttt) cc_final: 0.6519 (ttt)
REVERT: A   82 MET cc_start: 0.8017 (tmm) cc_final: 0.7423 (ttp)
REVERT: A   96 MET cc_start: 0.7535 (mtt) cc_final: 0.6698 (mmm)
REVERT: A   99 TRP cc_start: 0.8166 (t-100) cc_final: 0.7742 (t-100)
REVERT: A  223 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7145 (m-80)
REVERT: A  300 LYS cc_start: 0.8799 (tptm) cc_final: 0.7826 (ttpp)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.1188
  time to fit residues: 11.3255
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  385 ASN
Chi-restraints excluded: chain A residue  405 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.148881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.115827 restraints weight = 4349.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.61
r_work: 0.3378 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3097  Z= 0.142
  Angle     :  0.589   7.188   4209  Z= 0.302
  Chirality :  0.039   0.126    488
  Planarity :  0.003   0.021    515
  Dihedral  :  5.168  46.065    422
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.20 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.45), residues: 371
  helix:  1.68 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.65 (0.85), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.012   0.001   PHE A 208 
 TYR   0.040   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04390 (  244)
  hydrogen bonds       : angle       4.17534 (  732)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       2.31637 (    4)
  covalent geometry    : bond        0.00312 ( 3095)
  covalent geometry    : angle       0.58447 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6779 (ttt) cc_final: 0.6525 (ttt)
REVERT: A   82 MET cc_start: 0.7992 (tmm) cc_final: 0.7431 (ttp)
REVERT: A   96 MET cc_start: 0.7498 (mtt) cc_final: 0.6696 (mmm)
REVERT: A   99 TRP cc_start: 0.8176 (t-100) cc_final: 0.7717 (t-100)
REVERT: A  223 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7125 (m-80)
REVERT: A  300 LYS cc_start: 0.8792 (tptm) cc_final: 0.7812 (ttpp)
  outliers start: 12
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1202
  time to fit residues: 10.9103
Evaluate side-chains
  75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.114108 restraints weight = 4196.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.54
r_work: 0.3361 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3097  Z= 0.155
  Angle     :  0.601   6.671   4209  Z= 0.309
  Chirality :  0.039   0.126    488
  Planarity :  0.003   0.020    515
  Dihedral  :  5.202  44.332    422
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.50 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.45), residues: 371
  helix:  1.61 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.61 (0.85), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.013   0.001   PHE A 208 
 TYR   0.039   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  244)
  hydrogen bonds       : angle       4.20960 (  732)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       2.25458 (    4)
  covalent geometry    : bond        0.00344 ( 3095)
  covalent geometry    : angle       0.59732 ( 4205)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   36 MET cc_start: 0.6862 (ttt) cc_final: 0.6601 (ttt)
REVERT: A   82 MET cc_start: 0.7923 (tmm) cc_final: 0.7451 (ttp)
REVERT: A   96 MET cc_start: 0.7491 (mtt) cc_final: 0.6718 (mmm)
REVERT: A   99 TRP cc_start: 0.8192 (t-100) cc_final: 0.7706 (t-100)
REVERT: A  223 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (m-80)
REVERT: A  285 ARG cc_start: 0.6507 (mpt180) cc_final: 0.6273 (mpt180)
REVERT: A  300 LYS cc_start: 0.8757 (tptm) cc_final: 0.7779 (ttpp)
  outliers start: 11
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1239
  time to fit residues: 11.4219
Evaluate side-chains
  77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain A residue  385 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.148115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.115594 restraints weight = 4397.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.52
r_work: 0.3396 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3097  Z= 0.143
  Angle     :  0.591   5.744   4209  Z= 0.309
  Chirality :  0.039   0.136    488
  Planarity :  0.003   0.021    515
  Dihedral  :  5.208  46.050    422
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.50 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.44), residues: 371
  helix:  1.64 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.65 (0.86), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 237 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.013   0.001   PHE A 208 
 TYR   0.037   0.003   TYR A 324 
 ARG   0.001   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  244)
  hydrogen bonds       : angle       4.17689 (  732)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       2.32383 (    4)
  covalent geometry    : bond        0.00316 ( 3095)
  covalent geometry    : angle       0.58710 ( 4205)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1815.74 seconds
wall clock time: 32 minutes 12.63 seconds (1932.63 seconds total)