Starting phenix.real_space_refine
on Fri Aug 22 14:10:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx1_37897/08_2025/8wx1_37897.cif"
  }
  resolution = 3.64
  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=   0.002 sd=   0.038
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2593      2.51       5
     N     640      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  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: 3926
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3926
          Classifications: {'peptide': 500}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 474}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 1.24, per 1000 atoms: 0.32
  Number of scatterers: 3926
  At special positions: 0
  Unit cell: (79.68, 74.1467, 69.72, 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      23     16.00
     O     670      8.00
     N     640      7.00
     C    2593      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 523 " - pdb=" SG  CYS A 533 " 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: 0.33
  Conformation dependent library (CDL) restraints added in 154.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  926

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 1 sheets defined
      79.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 61
      removed outlier: 4.118A  pdb=" N   ASN A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   VAL A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 97
      Proline residue:  A  88  - end of helix
      removed outlier: 4.076A  pdb=" N   TYR A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 123
    Processing helix  chain 'A' and resid 123 through 131
      removed outlier: 3.586A  pdb=" N   CYS A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 187
    Processing helix  chain 'A' and resid 191 through 224
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 3.884A  pdb=" N   GLY A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 300 through 341
      Proline residue:  A 316  - end of helix
      Proline residue:  A 323  - end of helix
      removed outlier: 3.641A  pdb=" N   HIS A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 399
      removed outlier: 3.677A  pdb=" N   LEU A 383 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 384 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      Proline residue:  A 385  - end of helix
      Proline residue:  A 393  - end of helix
    Processing helix  chain 'A' and resid 403 through 435
      removed outlier: 3.597A  pdb=" N   ALA A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 457 through 483
      removed outlier: 4.556A  pdb=" N   GLN A 461 " --> pdb=" O   TRP A 457 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 488 through 515
    Processing helix  chain 'A' and resid 535 through 566
    Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 443
      removed outlier: 3.961A  pdb=" N   ILE A 443 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 446 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    939 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: 0.57

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1194
        1.34 -     1.46: 919
        1.46 -     1.58: 1879
        1.58 -     1.70: 0
        1.70 -     1.81: 37
  Bond restraints: 4029
  Sorted by residual:
  bond pdb=" C   SER A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.331  1.362 -0.031 1.27e-02 6.20e+03 5.85e+00
  bond pdb=" C   VAL A 322 "
       pdb=" N   PRO A 323 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.77e+00
  bond pdb=" C   ILE A 474 "
       pdb=" N   PRO A 475 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.19e+00
  bond pdb=" C   ALA A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.20e-02 6.94e+03 3.12e+00
  bond pdb=" C   LEU A 315 "
       pdb=" N   PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.87e+00
  ... (remaining 4024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 5103
        1.29 -     2.59: 298
        2.59 -     3.88: 59
        3.88 -     5.17: 20
        5.17 -     6.47: 7
  Bond angle restraints: 5487
  Sorted by residual:
  angle pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
        pdb=" C   VAL A 187 "
      ideal   model   delta    sigma   weight residual
     111.91  108.05    3.86 8.90e-01 1.26e+00 1.88e+01
  angle pdb=" C   GLN A 458 "
        pdb=" N   ILE A 459 "
        pdb=" CA  ILE A 459 "
      ideal   model   delta    sigma   weight residual
     120.33  123.30   -2.97 8.00e-01 1.56e+00 1.38e+01
  angle pdb=" C   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     113.70  110.40    3.30 9.50e-01 1.11e+00 1.21e+01
  angle pdb=" C   TRP A 152 "
        pdb=" N   SER A 153 "
        pdb=" CA  SER A 153 "
      ideal   model   delta    sigma   weight residual
     122.74  127.50   -4.76 1.44e+00 4.82e-01 1.09e+01
  angle pdb=" CA  ARG A 366 "
        pdb=" C   ARG A 366 "
        pdb=" N   ILE A 367 "
      ideal   model   delta    sigma   weight residual
     114.17  118.88   -4.71 1.45e+00 4.76e-01 1.05e+01
  ... (remaining 5482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2100
       17.16 -    34.33: 207
       34.33 -    51.49: 31
       51.49 -    68.66: 6
       68.66 -    85.82: 4
  Dihedral angle restraints: 2348
    sinusoidal: 906
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" CA  MET A 188 "
           pdb=" C   MET A 188 "
           pdb=" N   ASP A 189 "
           pdb=" CA  ASP A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.74  -32.26     0      5.00e+00 4.00e-02 4.16e+01
  dihedral pdb=" CA  CYS A 273 "
           pdb=" C   CYS A 273 "
           pdb=" N   PRO A 274 "
           pdb=" CA  PRO A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.53   16.47     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASN A 346 "
           pdb=" CB  ASN A 346 "
           pdb=" CG  ASN A 346 "
           pdb=" OD1 ASN A 346 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -174.37  -65.63     2      2.00e+01 2.50e-03 9.96e+00
  ... (remaining 2345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 436
       0.027 -    0.054: 100
       0.054 -    0.081: 68
       0.081 -    0.109: 20
       0.109 -    0.136: 5
  Chirality restraints: 629
  Sorted by residual:
  chirality pdb=" CA  ILE A 224 "
            pdb=" N   ILE A 224 "
            pdb=" C   ILE A 224 "
            pdb=" CB  ILE A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 344 "
            pdb=" N   ILE A 344 "
            pdb=" C   ILE A 344 "
            pdb=" CB  ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  PRO A 368 "
            pdb=" N   PRO A 368 "
            pdb=" C   PRO A 368 "
            pdb=" CB  PRO A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 626 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  26 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A  27 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 214 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" C   LEU A 214 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 214 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 215 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 439 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO A 440 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1147
        2.82 -     3.34: 4189
        3.34 -     3.86: 6800
        3.86 -     4.38: 7128
        4.38 -     4.90: 12352
  Nonbonded interactions: 31616
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  29 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER A 259 "
            pdb=" OG  SER A 259 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASP A 526 "
            pdb=" ND2 ASN A 529 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   PRO A 402 "
            pdb=" NZ  LYS A 407 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   MET A 188 "
            pdb=" N   LEU A 190 "
     model   vdw
     2.400 3.120
  ... (remaining 31611 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.090
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
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      :  0.003   0.031   4031  Z= 0.172
  Angle     :  0.737   6.466   5491  Z= 0.464
  Chirality :  0.035   0.136    629
  Planarity :  0.004   0.041    680
  Dihedral  : 13.802  85.821   1416
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.67 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.37), residues: 492
  helix:  0.75 (0.24), residues: 386
  sheet:  None (None), residues: 0
  loop : -2.47 (0.69), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 196 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.010   0.001   PHE A 479 
 TRP   0.014   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4029)
  covalent geometry    : angle       0.73729 ( 5487)
  SS BOND              : bond        0.00137 (    2)
  SS BOND              : angle       0.52657 (    4)
  hydrogen bonds       : bond        0.07212 (  314)
  hydrogen bonds       : angle       4.40436 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.8502 (tmm) cc_final: 0.8299 (tmm)
REVERT: A  303 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6771 (tm-30)
REVERT: A  474 ILE cc_start: 0.8674 (mm) cc_final: 0.8350 (mm)
REVERT: A  552 LEU cc_start: 0.8554 (tp) cc_final: 0.8319 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0640
  time to fit residues: 12.4167
Evaluate side-chains
  109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
A 330 GLN
A 346 ASN
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 565 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.180504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153564 restraints weight = 5413.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.157907 restraints weight = 2881.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160681 restraints weight = 1944.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.162507 restraints weight = 1516.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.163238 restraints weight = 1290.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4031  Z= 0.163
  Angle     :  0.685  10.821   5491  Z= 0.336
  Chirality :  0.040   0.187    629
  Planarity :  0.005   0.041    680
  Dihedral  :  4.371  26.421    540
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.88 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.66 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.40), residues: 492
  helix:  1.74 (0.26), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.68 (0.73), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  46 
 TYR   0.023   0.002   TYR A 481 
 PHE   0.026   0.002   PHE A 496 
 TRP   0.011   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4029)
  covalent geometry    : angle       0.68494 ( 5487)
  SS BOND              : bond        0.00555 (    2)
  SS BOND              : angle       0.41611 (    4)
  hydrogen bonds       : bond        0.04247 (  314)
  hydrogen bonds       : angle       4.24581 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7623 (tm-30)
REVERT: A  335 TYR cc_start: 0.8625 (m-10) cc_final: 0.8338 (m-10)
REVERT: A  552 LEU cc_start: 0.8642 (tp) cc_final: 0.8332 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 113
  average time/residue: 0.0537
  time to fit residues: 7.9834
Evaluate side-chains
  108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0980
   chunk 34 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.175984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148881 restraints weight = 5396.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153259 restraints weight = 2898.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156089 restraints weight = 1957.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.157932 restraints weight = 1525.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.159096 restraints weight = 1293.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4031  Z= 0.146
  Angle     :  0.632   8.423   5491  Z= 0.313
  Chirality :  0.040   0.205    629
  Planarity :  0.005   0.040    680
  Dihedral  :  4.282  24.689    540
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.49 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.05 %
    Favored  : 76.08 %
  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:  1.87 (0.40), residues: 492
  helix:  1.95 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -1.51 (0.74), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 192 
 TYR   0.012   0.001   TYR A 324 
 PHE   0.023   0.002   PHE A 527 
 TRP   0.011   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4029)
  covalent geometry    : angle       0.63236 ( 5487)
  SS BOND              : bond        0.00513 (    2)
  SS BOND              : angle       0.22481 (    4)
  hydrogen bonds       : bond        0.04354 (  314)
  hydrogen bonds       : angle       4.21936 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8710 (t0) cc_final: 0.8502 (t0)
REVERT: A  303 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: A  328 TYR cc_start: 0.8888 (t80) cc_final: 0.8679 (t80)
REVERT: A  335 TYR cc_start: 0.8628 (m-10) cc_final: 0.8214 (m-10)
REVERT: A  449 TYR cc_start: 0.7229 (m-80) cc_final: 0.6999 (m-80)
REVERT: A  527 PHE cc_start: 0.4612 (p90) cc_final: 0.4292 (p90)
REVERT: A  552 LEU cc_start: 0.8549 (tp) cc_final: 0.8306 (tt)
REVERT: A  561 GLU cc_start: 0.8340 (tp30) cc_final: 0.8112 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 112
  average time/residue: 0.0484
  time to fit residues: 7.3037
Evaluate side-chains
  110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 7 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   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 332 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.174449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147250 restraints weight = 5413.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151537 restraints weight = 2890.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.154448 restraints weight = 1955.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156105 restraints weight = 1517.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157344 restraints weight = 1299.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4031  Z= 0.141
  Angle     :  0.613   6.657   5491  Z= 0.308
  Chirality :  0.040   0.143    629
  Planarity :  0.005   0.040    680
  Dihedral  :  4.308  24.476    540
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.77 %
    Favored  : 73.68 %
  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:  2.07 (0.41), residues: 492
  helix:  2.08 (0.26), residues: 384
  sheet: -2.80 (1.27), residues: 10
  loop : -1.02 (0.82), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  31 
 TYR   0.015   0.001   TYR A 560 
 PHE   0.019   0.001   PHE A 496 
 TRP   0.018   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4029)
  covalent geometry    : angle       0.61274 ( 5487)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.32411 (    4)
  hydrogen bonds       : bond        0.04323 (  314)
  hydrogen bonds       : angle       4.20864 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8555 (tp) cc_final: 0.8320 (tp)
REVERT: A  185 ASP cc_start: 0.8769 (t0) cc_final: 0.8493 (t0)
REVERT: A  303 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: A  328 TYR cc_start: 0.8878 (t80) cc_final: 0.8383 (t80)
REVERT: A  335 TYR cc_start: 0.8606 (m-10) cc_final: 0.8289 (m-10)
REVERT: A  552 LEU cc_start: 0.8620 (tp) cc_final: 0.8392 (tt)
  outliers start: 19
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0522
  time to fit residues: 7.3367
Evaluate side-chains
  103 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0670
   chunk 28 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.175310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147781 restraints weight = 5455.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152128 restraints weight = 2959.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.154909 restraints weight = 2019.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156641 restraints weight = 1589.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.157851 restraints weight = 1363.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4031  Z= 0.132
  Angle     :  0.609   6.720   5491  Z= 0.301
  Chirality :  0.040   0.175    629
  Planarity :  0.005   0.039    680
  Dihedral  :  4.236  21.942    540
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.21 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.25 (0.41), residues: 492
  helix:  2.18 (0.27), residues: 384
  sheet: -2.60 (1.37), residues: 10
  loop : -0.84 (0.83), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 429 
 TYR   0.021   0.001   TYR A 156 
 PHE   0.027   0.001   PHE A 527 
 TRP   0.019   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4029)
  covalent geometry    : angle       0.60907 ( 5487)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       0.36105 (    4)
  hydrogen bonds       : bond        0.04214 (  314)
  hydrogen bonds       : angle       4.19491 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8716 (t0) cc_final: 0.8396 (t0)
REVERT: A  303 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: A  328 TYR cc_start: 0.8888 (t80) cc_final: 0.8427 (t80)
REVERT: A  335 TYR cc_start: 0.8592 (m-10) cc_final: 0.8324 (m-10)
REVERT: A  552 LEU cc_start: 0.8577 (tp) cc_final: 0.8334 (tt)
REVERT: A  561 GLU cc_start: 0.8297 (tp30) cc_final: 0.7991 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0397
  time to fit residues: 5.7796
Evaluate side-chains
  107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8880

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.170161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.142455 restraints weight = 5535.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146604 restraints weight = 2986.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149318 restraints weight = 2048.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150962 restraints weight = 1615.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.152192 restraints weight = 1392.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4031  Z= 0.163
  Angle     :  0.639   7.278   5491  Z= 0.321
  Chirality :  0.041   0.150    629
  Planarity :  0.006   0.077    680
  Dihedral  :  4.281  20.668    540
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 24.16 %
    Favored  : 71.53 %
  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:  2.20 (0.41), residues: 492
  helix:  2.14 (0.26), residues: 382
  sheet: -2.02 (1.65), residues: 10
  loop : -0.85 (0.82), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 429 
 TYR   0.011   0.001   TYR A 560 
 PHE   0.029   0.002   PHE A 527 
 TRP   0.023   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4029)
  covalent geometry    : angle       0.63929 ( 5487)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       0.49108 (    4)
  hydrogen bonds       : bond        0.04556 (  314)
  hydrogen bonds       : angle       4.32558 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8590 (tp) cc_final: 0.8358 (tp)
REVERT: A  185 ASP cc_start: 0.8705 (t0) cc_final: 0.8342 (t0)
REVERT: A  303 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: A  328 TYR cc_start: 0.8935 (t80) cc_final: 0.8434 (t80)
REVERT: A  335 TYR cc_start: 0.8665 (m-10) cc_final: 0.8368 (m-10)
REVERT: A  454 SER cc_start: 0.7566 (m) cc_final: 0.7329 (t)
REVERT: A  481 TYR cc_start: 0.8893 (t80) cc_final: 0.8540 (t80)
REVERT: A  527 PHE cc_start: 0.5107 (p90) cc_final: 0.4858 (p90)
REVERT: A  561 GLU cc_start: 0.8279 (tp30) cc_final: 0.7998 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0393
  time to fit residues: 5.9492
Evaluate side-chains
  112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   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 330 GLN
A 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.170785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.142670 restraints weight = 5583.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146772 restraints weight = 3004.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149564 restraints weight = 2061.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151297 restraints weight = 1620.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152523 restraints weight = 1391.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4031  Z= 0.151
  Angle     :  0.658  10.636   5491  Z= 0.324
  Chirality :  0.041   0.184    629
  Planarity :  0.005   0.060    680
  Dihedral  :  4.289  19.341    540
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.30 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 25.84 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.41), residues: 492
  helix:  2.18 (0.26), residues: 383
  sheet: -1.52 (1.87), residues: 10
  loop : -0.95 (0.82), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  31 
 TYR   0.010   0.001   TYR A 156 
 PHE   0.024   0.001   PHE A 527 
 TRP   0.016   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4029)
  covalent geometry    : angle       0.65816 ( 5487)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       0.50791 (    4)
  hydrogen bonds       : bond        0.04438 (  314)
  hydrogen bonds       : angle       4.30876 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8720 (t0) cc_final: 0.8362 (t0)
REVERT: A  303 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: A  328 TYR cc_start: 0.8951 (t80) cc_final: 0.8480 (t80)
REVERT: A  335 TYR cc_start: 0.8646 (m-10) cc_final: 0.8325 (m-10)
REVERT: A  449 TYR cc_start: 0.7379 (m-80) cc_final: 0.7142 (m-80)
REVERT: A  454 SER cc_start: 0.7629 (m) cc_final: 0.7387 (t)
REVERT: A  481 TYR cc_start: 0.8832 (t80) cc_final: 0.8501 (t80)
REVERT: A  561 GLU cc_start: 0.8284 (tp30) cc_final: 0.8001 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0378
  time to fit residues: 5.8066
Evaluate side-chains
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   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 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.171232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.143863 restraints weight = 5443.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147948 restraints weight = 2941.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150599 restraints weight = 2011.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152390 restraints weight = 1590.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152789 restraints weight = 1363.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4031  Z= 0.152
  Angle     :  0.661  10.365   5491  Z= 0.330
  Chirality :  0.042   0.189    629
  Planarity :  0.005   0.048    680
  Dihedral  :  4.326  20.564    540
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.08 %
    Favored  : 69.86 %
  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:  2.27 (0.41), residues: 492
  helix:  2.18 (0.26), residues: 383
  sheet: -1.35 (1.98), residues: 10
  loop : -0.93 (0.81), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  31 
 TYR   0.018   0.001   TYR A 156 
 PHE   0.017   0.001   PHE A 496 
 TRP   0.015   0.001   TRP A  30 
 HIS   0.001   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4029)
  covalent geometry    : angle       0.66070 ( 5487)
  SS BOND              : bond        0.00177 (    2)
  SS BOND              : angle       0.59265 (    4)
  hydrogen bonds       : bond        0.04468 (  314)
  hydrogen bonds       : angle       4.32383 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.8004 (m-30) cc_final: 0.7469 (t0)
REVERT: A  185 ASP cc_start: 0.8722 (t0) cc_final: 0.8355 (t0)
REVERT: A  303 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: A  335 TYR cc_start: 0.8641 (m-10) cc_final: 0.8341 (m-10)
REVERT: A  454 SER cc_start: 0.7655 (m) cc_final: 0.7418 (t)
REVERT: A  481 TYR cc_start: 0.8832 (t80) cc_final: 0.8436 (t80)
REVERT: A  561 GLU cc_start: 0.8257 (tp30) cc_final: 0.7970 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0458
  time to fit residues: 7.0142
Evaluate side-chains
  119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  506 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0670
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.172102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144548 restraints weight = 5498.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.148592 restraints weight = 2925.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.151474 restraints weight = 1994.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.153277 restraints weight = 1563.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.154313 restraints weight = 1337.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   4031  Z= 0.139
  Angle     :  0.651   9.516   5491  Z= 0.325
  Chirality :  0.041   0.183    629
  Planarity :  0.005   0.060    680
  Dihedral  :  4.285  18.762    540
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.30 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 27.99 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.32 (0.41), residues: 492
  helix:  2.20 (0.27), residues: 383
  sheet: -1.23 (1.94), residues: 10
  loop : -0.83 (0.82), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 429 
 TYR   0.010   0.001   TYR A 324 
 PHE   0.016   0.001   PHE A 496 
 TRP   0.015   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4029)
  covalent geometry    : angle       0.65138 ( 5487)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       0.51780 (    4)
  hydrogen bonds       : bond        0.04335 (  314)
  hydrogen bonds       : angle       4.29117 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7921 (m-30) cc_final: 0.7427 (t0)
REVERT: A  185 ASP cc_start: 0.8729 (t0) cc_final: 0.8375 (t0)
REVERT: A  303 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: A  335 TYR cc_start: 0.8599 (m-10) cc_final: 0.8254 (m-10)
REVERT: A  454 SER cc_start: 0.7615 (m) cc_final: 0.7387 (t)
REVERT: A  481 TYR cc_start: 0.8775 (t80) cc_final: 0.8447 (t80)
REVERT: A  561 GLU cc_start: 0.8295 (tp30) cc_final: 0.8009 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 112
  average time/residue: 0.0395
  time to fit residues: 6.1604
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0170
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.172387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145202 restraints weight = 5440.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149479 restraints weight = 2863.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.152350 restraints weight = 1935.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.154007 restraints weight = 1510.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.155220 restraints weight = 1299.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4031  Z= 0.142
  Angle     :  0.667  10.142   5491  Z= 0.328
  Chirality :  0.041   0.174    629
  Planarity :  0.006   0.066    680
  Dihedral  :  4.313  20.110    540
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.71 %
    Favored  : 68.42 %
  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:  2.33 (0.41), residues: 492
  helix:  2.19 (0.27), residues: 383
  sheet: -1.17 (1.92), residues: 10
  loop : -0.76 (0.81), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 429 
 TYR   0.010   0.001   TYR A 324 
 PHE   0.016   0.001   PHE A 496 
 TRP   0.015   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4029)
  covalent geometry    : angle       0.66743 ( 5487)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.56624 (    4)
  hydrogen bonds       : bond        0.04331 (  314)
  hydrogen bonds       : angle       4.31952 (  939)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7918 (m-30) cc_final: 0.7429 (t0)
REVERT: A  185 ASP cc_start: 0.8712 (t0) cc_final: 0.8350 (t0)
REVERT: A  303 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7690 (tm-30)
REVERT: A  335 TYR cc_start: 0.8620 (m-10) cc_final: 0.8325 (m-10)
REVERT: A  454 SER cc_start: 0.7654 (m) cc_final: 0.7425 (t)
REVERT: A  481 TYR cc_start: 0.8763 (t80) cc_final: 0.8419 (t80)
REVERT: A  561 GLU cc_start: 0.8273 (tp30) cc_final: 0.7987 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0308
  time to fit residues: 4.6995
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0970
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.144656 restraints weight = 5442.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148769 restraints weight = 2870.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.151696 restraints weight = 1943.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.153285 restraints weight = 1515.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.154516 restraints weight = 1304.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4031  Z= 0.148
  Angle     :  0.673   9.184   5491  Z= 0.334
  Chirality :  0.042   0.174    629
  Planarity :  0.005   0.058    680
  Dihedral  :  4.293  18.056    540
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.69 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.71 %
    Favored  : 68.42 %
  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:  2.32 (0.41), residues: 492
  helix:  2.20 (0.27), residues: 383
  sheet: -1.05 (1.89), residues: 10
  loop : -0.88 (0.81), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  31 
 TYR   0.011   0.001   TYR A 324 
 PHE   0.015   0.001   PHE A 496 
 TRP   0.016   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4029)
  covalent geometry    : angle       0.67297 ( 5487)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.70013 (    4)
  hydrogen bonds       : bond        0.04361 (  314)
  hydrogen bonds       : angle       4.32780 (  939)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 745.62 seconds
wall clock time: 13 minutes 36.97 seconds (816.97 seconds total)