Starting phenix.real_space_refine
on Fri Aug 22 13:29:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c03_16354/08_2025/8c03_16354.map"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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      26      5.16       5
     C    2187      2.51       5
     N     542      2.21       5
     O     574      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3330
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3300
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 9, 'TRANS': 419}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'SZU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.21, per 1000 atoms: 0.36
  Number of scatterers: 3330
  At special positions: 0
  Unit cell: (78.12, 67.704, 84.63, 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      26     16.00
     F       1      9.00
     O     574      8.00
     N     542      7.00
     C    2187      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 129.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      92.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 54
      removed outlier: 3.767A  pdb=" N   GLY A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 86
      removed outlier: 3.634A  pdb=" N   GLY A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER A  71 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ALA A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.782A  pdb=" N   ALA A  92 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 3.723A  pdb=" N   LEU A 121 " --> pdb=" O   LYS A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 156
      removed outlier: 3.826A  pdb=" N   LEU A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 164
    Processing helix  chain 'A' and resid 166 through 199
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
      removed outlier: 3.742A  pdb=" N   GLY A 206 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 208 " --> pdb=" O   GLY A 204 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER A 209 " --> pdb=" O   CYS A 205 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 230 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 234
    Processing helix  chain 'A' and resid 288 through 305
    Processing helix  chain 'A' and resid 307 through 319
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 338 through 367
    Processing helix  chain 'A' and resid 369 through 393
    Processing helix  chain 'A' and resid 451 through 483
    Processing helix  chain 'A' and resid 485 through 487
      No H-bonds generated for 'chain 'A' and resid 485 through 487'
    Processing helix  chain 'A' and resid 488 through 514
      removed outlier: 3.815A  pdb=" N   ASN A 493 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 546
      removed outlier: 4.118A  pdb=" N   LEU A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    921 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: 0.69

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1028
        1.34 -     1.46: 824
        1.46 -     1.58: 1505
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 3401
  Sorted by residual:
  bond pdb=" C1  SZU A 601 "
       pdb=" C8  SZU A 601 "
    ideal  model  delta    sigma   weight residual
    1.476  1.325  0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" C2  SZU A 601 "
       pdb=" C3  SZU A 601 "
    ideal  model  delta    sigma   weight residual
    1.517  1.377  0.140 2.00e-02 2.50e+03 4.92e+01
  bond pdb=" C16 SZU A 601 "
       pdb=" C21 SZU A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.335  0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" C8  SZU A 601 "
       pdb=" N6  SZU A 601 "
    ideal  model  delta    sigma   weight residual
    1.396  1.329  0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" C20 SZU A 601 "
       pdb=" C21 SZU A 601 "
    ideal  model  delta    sigma   weight residual
    1.395  1.328  0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 3396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 4565
        2.51 -     5.03: 58
        5.03 -     7.54: 2
        7.54 -    10.06: 1
       10.06 -    12.57: 1
  Bond angle restraints: 4627
  Sorted by residual:
  angle pdb=" C3  SZU A 601 "
        pdb=" C2  SZU A 601 "
        pdb=" N1  SZU A 601 "
      ideal   model   delta    sigma   weight residual
     113.72  101.15   12.57 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" N   GLN A 496 "
        pdb=" CA  GLN A 496 "
        pdb=" C   GLN A 496 "
      ideal   model   delta    sigma   weight residual
     111.36  106.91    4.45 1.09e+00 8.42e-01 1.67e+01
  angle pdb=" N   LEU A  59 "
        pdb=" CA  LEU A  59 "
        pdb=" C   LEU A  59 "
      ideal   model   delta    sigma   weight residual
     111.11  106.50    4.61 1.20e+00 6.94e-01 1.48e+01
  angle pdb=" CA  THR A 334 "
        pdb=" C   THR A 334 "
        pdb=" O   THR A 334 "
      ideal   model   delta    sigma   weight residual
     120.90  117.00    3.90 1.03e+00 9.43e-01 1.43e+01
  angle pdb=" N   PHE A 324 "
        pdb=" CA  PHE A 324 "
        pdb=" C   PHE A 324 "
      ideal   model   delta    sigma   weight residual
     111.71  106.79    4.92 1.34e+00 5.57e-01 1.35e+01
  ... (remaining 4622 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 1769
       14.30 -    28.61: 130
       28.61 -    42.91: 44
       42.91 -    57.21: 17
       57.21 -    71.52: 6
  Dihedral angle restraints: 1966
    sinusoidal: 737
      harmonic: 1229
  Sorted by residual:
  dihedral pdb=" N   GLU A 518 "
           pdb=" CA  GLU A 518 "
           pdb=" CB  GLU A 518 "
           pdb=" CG  GLU A 518 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.88   59.88     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ILE A 186 "
           pdb=" CB  ILE A 186 "
           pdb=" CG1 ILE A 186 "
           pdb=" CD1 ILE A 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  123.89   56.11     3      1.50e+01 4.44e-03 9.38e+00
  dihedral pdb=" N   ILE A  78 "
           pdb=" CA  ILE A  78 "
           pdb=" CB  ILE A  78 "
           pdb=" CG1 ILE A  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.35   54.35     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 1963 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 473
       0.052 -    0.104: 74
       0.104 -    0.156: 9
       0.156 -    0.208: 3
       0.208 -    0.260: 1
  Chirality restraints: 560
  Sorted by residual:
  chirality pdb=" CA  LEU A  59 "
            pdb=" N   LEU A  59 "
            pdb=" C   LEU A  59 "
            pdb=" CB  LEU A  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  TYR A 333 "
            pdb=" N   TYR A 333 "
            pdb=" C   TYR A 333 "
            pdb=" CB  TYR A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" CA  PHE A 324 "
            pdb=" N   PHE A 324 "
            pdb=" C   PHE A 324 "
            pdb=" CB  PHE A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 557 not shown)

  Planarity restraints: 556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  53 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   LEU A  53 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU A  53 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A  54 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 324 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.75e+00
        pdb=" C   PHE A 324 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 324 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 325 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  SZU A 601 "   -0.004 2.00e-02 2.50e+03   1.42e-02 2.53e+00
        pdb=" C2  SZU A 601 "    0.016 2.00e-02 2.50e+03
        pdb=" C8  SZU A 601 "    0.013 2.00e-02 2.50e+03
        pdb=" N1  SZU A 601 "   -0.023 2.00e-02 2.50e+03
        pdb=" O1  SZU A 601 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 553 not shown)

  Histogram of nonbonded interaction distances:
        1.23 -     1.97: 1
        1.97 -     2.70: 81
        2.70 -     3.43: 5414
        3.43 -     4.17: 7309
        4.17 -     4.90: 13846
  Nonbonded interactions: 26651
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 302 "
            pdb=" OE1 GLN A 496 "
     model   vdw
     1.232 3.040
  nonbonded pdb=" CD1 LEU A 469 "
            pdb=" F1  SZU A 601 "
     model   vdw
     2.141 3.410
  nonbonded pdb=" O   TYR A  20 "
            pdb=" OG  SER A  23 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASN A  86 "
            pdb=" NZ  LYS A 236 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   LEU A 369 "
            pdb=" OG1 THR A 372 "
     model   vdw
     2.260 3.040
  ... (remaining 26646 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.000
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
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      :  0.006   0.151   3401  Z= 0.345
  Angle     :  0.670  12.575   4627  Z= 0.403
  Chirality :  0.040   0.260    560
  Planarity :  0.003   0.017    556
  Dihedral  : 13.116  71.516   1178
  Min Nonbonded Distance : 1.232

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  :  8.08 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.41), residues: 423
  helix:  2.29 (0.26), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.88 (0.85), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  88 
 TYR   0.006   0.001   TYR A 220 
 PHE   0.008   0.001   PHE A 508 
 TRP   0.004   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 3401)
  covalent geometry    : angle       0.67009 ( 4627)
  hydrogen bonds       : bond        0.13852 (  308)
  hydrogen bonds       : angle       5.29252 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 LYS cc_start: 0.7974 (tptt) cc_final: 0.7486 (tppt)
REVERT: A  100 ASN cc_start: 0.7632 (m-40) cc_final: 0.6463 (m-40)
REVERT: A  216 MET cc_start: 0.8280 (tpt) cc_final: 0.7927 (tpp)
REVERT: A  319 MET cc_start: 0.7296 (ttt) cc_final: 0.6954 (tmm)
  outliers start: 11
  outliers final: 2
  residues processed: 138
  average time/residue: 0.0646
  time to fit residues: 11.0356
Evaluate side-chains
  100 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  174 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 194 GLN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.177819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142807 restraints weight = 4783.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.147527 restraints weight = 3008.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.150302 restraints weight = 2277.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.152486 restraints weight = 1931.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153531 restraints weight = 1714.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3401  Z= 0.152
  Angle     :  0.575   6.886   4627  Z= 0.296
  Chirality :  0.038   0.132    560
  Planarity :  0.004   0.029    556
  Dihedral  :  7.383  75.216    474
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.99 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.40), residues: 423
  helix:  2.31 (0.25), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.13 (1.03), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 293 
 TYR   0.014   0.002   TYR A  29 
 PHE   0.027   0.002   PHE A 308 
 TRP   0.009   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3401)
  covalent geometry    : angle       0.57489 ( 4627)
  hydrogen bonds       : bond        0.05085 (  308)
  hydrogen bonds       : angle       4.30386 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   57 SER cc_start: 0.8360 (m) cc_final: 0.8009 (p)
REVERT: A   90 LYS cc_start: 0.8019 (tptt) cc_final: 0.7480 (tppt)
REVERT: A  166 ASP cc_start: 0.8130 (t0) cc_final: 0.7738 (t0)
REVERT: A  173 MET cc_start: 0.7604 (ttm) cc_final: 0.7261 (ttm)
REVERT: A  319 MET cc_start: 0.7554 (ttt) cc_final: 0.7122 (tmm)
REVERT: A  366 LYS cc_start: 0.8331 (tptt) cc_final: 0.7852 (mmmt)
REVERT: A  469 LEU cc_start: 0.8908 (tp) cc_final: 0.8605 (tp)
  outliers start: 13
  outliers final: 3
  residues processed: 116
  average time/residue: 0.0573
  time to fit residues: 8.2614
Evaluate side-chains
  103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  221 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0000
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.175384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140443 restraints weight = 4757.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145143 restraints weight = 2966.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.148468 restraints weight = 2227.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.150102 restraints weight = 1838.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.151740 restraints weight = 1648.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3401  Z= 0.142
  Angle     :  0.568   7.487   4627  Z= 0.291
  Chirality :  0.038   0.162    560
  Planarity :  0.003   0.031    556
  Dihedral  :  6.875  74.209    470
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.33 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.40), residues: 423
  helix:  2.28 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.09 (1.08), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  40 
 TYR   0.021   0.002   TYR A  29 
 PHE   0.023   0.002   PHE A 308 
 TRP   0.006   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3401)
  covalent geometry    : angle       0.56816 ( 4627)
  hydrogen bonds       : bond        0.04769 (  308)
  hydrogen bonds       : angle       4.12347 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   57 SER cc_start: 0.8074 (m) cc_final: 0.7761 (p)
REVERT: A  145 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8148 (tp)
REVERT: A  166 ASP cc_start: 0.8089 (t0) cc_final: 0.7628 (t0)
REVERT: A  173 MET cc_start: 0.7493 (ttm) cc_final: 0.7196 (ttm)
REVERT: A  319 MET cc_start: 0.7639 (ttt) cc_final: 0.7182 (tmm)
REVERT: A  366 LYS cc_start: 0.8398 (tptt) cc_final: 0.7962 (mmmt)
REVERT: A  543 GLN cc_start: 0.8015 (mm110) cc_final: 0.7688 (mm-40)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.0561
  time to fit residues: 7.7822
Evaluate side-chains
  109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  342 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
A 100 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 507 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.178405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144165 restraints weight = 4706.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.148696 restraints weight = 2978.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.151732 restraints weight = 2265.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153171 restraints weight = 1903.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154620 restraints weight = 1723.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3401  Z= 0.148
  Angle     :  0.595   6.759   4627  Z= 0.300
  Chirality :  0.039   0.142    560
  Planarity :  0.003   0.033    556
  Dihedral  :  6.779  73.602    470
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 19.22 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.03 (0.40), residues: 423
  helix:  2.33 (0.26), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.46 (1.01), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.029   0.002   TYR A  29 
 PHE   0.037   0.002   PHE A 308 
 TRP   0.006   0.001   TRP A  42 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3401)
  covalent geometry    : angle       0.59479 ( 4627)
  hydrogen bonds       : bond        0.04718 (  308)
  hydrogen bonds       : angle       4.10288 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  100 ASN cc_start: 0.8224 (m110) cc_final: 0.7227 (m-40)
REVERT: A  145 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8193 (tp)
REVERT: A  166 ASP cc_start: 0.8080 (t0) cc_final: 0.7643 (t0)
REVERT: A  173 MET cc_start: 0.7355 (ttm) cc_final: 0.7124 (ttm)
REVERT: A  319 MET cc_start: 0.7711 (ttt) cc_final: 0.7204 (tmm)
REVERT: A  366 LYS cc_start: 0.8358 (tptt) cc_final: 0.7943 (mmmt)
REVERT: A  543 GLN cc_start: 0.8014 (mm110) cc_final: 0.7694 (mm-40)
  outliers start: 19
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0445
  time to fit residues: 6.3573
Evaluate side-chains
  109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  507 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.176211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141731 restraints weight = 4781.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146225 restraints weight = 3028.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.148898 restraints weight = 2308.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151167 restraints weight = 1954.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.152271 restraints weight = 1731.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3401  Z= 0.162
  Angle     :  0.622   7.442   4627  Z= 0.313
  Chirality :  0.039   0.183    560
  Planarity :  0.003   0.032    556
  Dihedral  :  6.682  72.125    470
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 21.45 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.91 (0.40), residues: 423
  helix:  2.23 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.44 (1.01), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.021   0.001   TYR A  29 
 PHE   0.031   0.002   PHE A 308 
 TRP   0.006   0.001   TRP A 470 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3401)
  covalent geometry    : angle       0.62219 ( 4627)
  hydrogen bonds       : bond        0.04765 (  308)
  hydrogen bonds       : angle       4.13118 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8234 (tp)
REVERT: A  166 ASP cc_start: 0.8019 (t0) cc_final: 0.7559 (t0)
REVERT: A  173 MET cc_start: 0.7478 (ttm) cc_final: 0.7227 (ttm)
REVERT: A  319 MET cc_start: 0.7766 (ttt) cc_final: 0.7187 (tmm)
REVERT: A  366 LYS cc_start: 0.8394 (tptt) cc_final: 0.7924 (mmmt)
REVERT: A  504 ASP cc_start: 0.8060 (t70) cc_final: 0.7666 (t0)
REVERT: A  543 GLN cc_start: 0.8015 (mm110) cc_final: 0.7634 (mm-40)
  outliers start: 19
  outliers final: 14
  residues processed: 107
  average time/residue: 0.0466
  time to fit residues: 6.3443
Evaluate side-chains
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  174 ASN
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  475 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142935 restraints weight = 4792.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.147303 restraints weight = 3047.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.149936 restraints weight = 2332.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.152165 restraints weight = 1981.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.152988 restraints weight = 1758.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3401  Z= 0.147
  Angle     :  0.623   8.005   4627  Z= 0.313
  Chirality :  0.040   0.182    560
  Planarity :  0.003   0.030    556
  Dihedral  :  6.572  70.496    470
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 23.40 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.40), residues: 423
  helix:  2.29 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.43 (1.00), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.023   0.002   TYR A  29 
 PHE   0.028   0.001   PHE A 308 
 TRP   0.005   0.001   TRP A 299 
 HIS   0.004   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3401)
  covalent geometry    : angle       0.62290 ( 4627)
  hydrogen bonds       : bond        0.04686 (  308)
  hydrogen bonds       : angle       4.08743 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8211 (tp)
REVERT: A  166 ASP cc_start: 0.8030 (t0) cc_final: 0.7605 (t0)
REVERT: A  173 MET cc_start: 0.7521 (ttm) cc_final: 0.7289 (ttm)
REVERT: A  202 VAL cc_start: 0.8492 (m) cc_final: 0.8285 (p)
REVERT: A  319 MET cc_start: 0.7723 (ttt) cc_final: 0.7194 (tmm)
REVERT: A  366 LYS cc_start: 0.8418 (tptt) cc_final: 0.7948 (mmmt)
REVERT: A  392 PHE cc_start: 0.8161 (t80) cc_final: 0.7898 (t80)
REVERT: A  504 ASP cc_start: 0.8034 (t70) cc_final: 0.7674 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0429
  time to fit residues: 5.8503
Evaluate side-chains
  108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  475 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 40 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.179113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.144841 restraints weight = 4782.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.149465 restraints weight = 3036.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152297 restraints weight = 2298.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.154510 restraints weight = 1934.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.155774 restraints weight = 1714.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3401  Z= 0.133
  Angle     :  0.596   7.772   4627  Z= 0.301
  Chirality :  0.039   0.186    560
  Planarity :  0.003   0.030    556
  Dihedral  :  6.432  69.439    470
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.91 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.40), residues: 423
  helix:  2.39 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.72 (0.98), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.022   0.001   TYR A  29 
 PHE   0.027   0.001   PHE A 308 
 TRP   0.005   0.001   TRP A  82 
 HIS   0.003   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3401)
  covalent geometry    : angle       0.59628 ( 4627)
  hydrogen bonds       : bond        0.04456 (  308)
  hydrogen bonds       : angle       3.95259 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8108 (tp)
REVERT: A  173 MET cc_start: 0.7518 (ttm) cc_final: 0.7217 (ttm)
REVERT: A  319 MET cc_start: 0.7621 (ttt) cc_final: 0.6942 (tmm)
REVERT: A  366 LYS cc_start: 0.8478 (tptt) cc_final: 0.7994 (mmmt)
REVERT: A  392 PHE cc_start: 0.8060 (t80) cc_final: 0.7820 (t80)
REVERT: A  504 ASP cc_start: 0.7961 (t70) cc_final: 0.7610 (t0)
REVERT: A  543 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7821 (mp10)
  outliers start: 12
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0523
  time to fit residues: 6.7622
Evaluate side-chains
  103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  475 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0270
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
A 125 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.178658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.143944 restraints weight = 4861.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.148367 restraints weight = 3078.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.151484 restraints weight = 2350.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153579 restraints weight = 1971.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.154002 restraints weight = 1750.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3401  Z= 0.140
  Angle     :  0.599   9.384   4627  Z= 0.302
  Chirality :  0.039   0.179    560
  Planarity :  0.003   0.030    556
  Dihedral  :  6.365  67.899    470
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.91 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.08 (0.40), residues: 423
  helix:  2.37 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.71 (0.99), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.023   0.001   TYR A  29 
 PHE   0.023   0.001   PHE A 308 
 TRP   0.020   0.001   TRP A  42 
 HIS   0.005   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3401)
  covalent geometry    : angle       0.59922 ( 4627)
  hydrogen bonds       : bond        0.04509 (  308)
  hydrogen bonds       : angle       3.98592 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8325 (mmm) cc_final: 0.7867 (mmp)
REVERT: A  145 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8122 (tp)
REVERT: A  166 ASP cc_start: 0.8034 (t0) cc_final: 0.7592 (t0)
REVERT: A  173 MET cc_start: 0.7374 (ttm) cc_final: 0.7058 (ttm)
REVERT: A  202 VAL cc_start: 0.8498 (m) cc_final: 0.8282 (p)
REVERT: A  319 MET cc_start: 0.7657 (ttt) cc_final: 0.7172 (tmm)
REVERT: A  366 LYS cc_start: 0.8462 (tptt) cc_final: 0.7986 (mmmt)
REVERT: A  392 PHE cc_start: 0.8106 (t80) cc_final: 0.7866 (t80)
REVERT: A  543 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7876 (mm-40)
  outliers start: 17
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0523
  time to fit residues: 6.6604
Evaluate side-chains
  104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  475 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0770
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.177666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.143191 restraints weight = 4835.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.147677 restraints weight = 3072.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.150037 restraints weight = 2337.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.152610 restraints weight = 1997.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.153830 restraints weight = 1761.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3401  Z= 0.146
  Angle     :  0.623   9.970   4627  Z= 0.309
  Chirality :  0.040   0.185    560
  Planarity :  0.003   0.030    556
  Dihedral  :  6.359  66.883    470
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 26.46 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.40), residues: 423
  helix:  2.36 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.45 (1.00), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  40 
 TYR   0.014   0.001   TYR A  29 
 PHE   0.021   0.002   PHE A 308 
 TRP   0.010   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3401)
  covalent geometry    : angle       0.62297 ( 4627)
  hydrogen bonds       : bond        0.04523 (  308)
  hydrogen bonds       : angle       4.00830 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8245 (mmm) cc_final: 0.7823 (mmp)
REVERT: A  145 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8128 (tp)
REVERT: A  173 MET cc_start: 0.7252 (ttm) cc_final: 0.7013 (ttm)
REVERT: A  202 VAL cc_start: 0.8401 (m) cc_final: 0.8157 (p)
REVERT: A  319 MET cc_start: 0.7583 (ttt) cc_final: 0.7062 (tmm)
REVERT: A  366 LYS cc_start: 0.8442 (tptt) cc_final: 0.7968 (mmmt)
REVERT: A  392 PHE cc_start: 0.8104 (t80) cc_final: 0.7867 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0527
  time to fit residues: 6.6907
Evaluate side-chains
  107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  475 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 34 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.178370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.144485 restraints weight = 4855.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148940 restraints weight = 3084.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.151770 restraints weight = 2351.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.154036 restraints weight = 1982.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155230 restraints weight = 1750.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3401  Z= 0.148
  Angle     :  0.636  10.620   4627  Z= 0.314
  Chirality :  0.040   0.188    560
  Planarity :  0.003   0.031    556
  Dihedral  :  6.325  65.498    470
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.18 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.40), residues: 423
  helix:  2.29 (0.26), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.76 (0.98), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.009   0.001   TYR A  29 
 PHE   0.020   0.002   PHE A 308 
 TRP   0.018   0.001   TRP A  42 
 HIS   0.005   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3401)
  covalent geometry    : angle       0.63578 ( 4627)
  hydrogen bonds       : bond        0.04566 (  308)
  hydrogen bonds       : angle       4.04109 (  921)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8221 (mmm) cc_final: 0.7982 (mmp)
REVERT: A  145 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8107 (tp)
REVERT: A  166 ASP cc_start: 0.8043 (t0) cc_final: 0.7603 (t0)
REVERT: A  202 VAL cc_start: 0.8299 (m) cc_final: 0.8011 (t)
REVERT: A  319 MET cc_start: 0.7507 (ttt) cc_final: 0.7029 (tmm)
REVERT: A  366 LYS cc_start: 0.8455 (tptt) cc_final: 0.8014 (mmmt)
REVERT: A  392 PHE cc_start: 0.8092 (t80) cc_final: 0.7883 (t80)
REVERT: A  486 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7637 (tp30)
  outliers start: 18
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0488
  time to fit residues: 6.2161
Evaluate side-chains
  104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  486 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.178897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.144860 restraints weight = 4896.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149430 restraints weight = 3138.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152606 restraints weight = 2378.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.154120 restraints weight = 1982.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.155733 restraints weight = 1782.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3401  Z= 0.150
  Angle     :  0.644  10.371   4627  Z= 0.320
  Chirality :  0.040   0.196    560
  Planarity :  0.003   0.030    556
  Dihedral  :  6.291  64.261    470
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 26.46 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.97 (0.41), residues: 423
  helix:  2.28 (0.26), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.42 (0.99), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  40 
 TYR   0.007   0.001   TYR A  29 
 PHE   0.023   0.002   PHE A 292 
 TRP   0.008   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3401)
  covalent geometry    : angle       0.64448 ( 4627)
  hydrogen bonds       : bond        0.04571 (  308)
  hydrogen bonds       : angle       4.03240 (  921)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 735.19 seconds
wall clock time: 13 minutes 21.57 seconds (801.57 seconds total)