Starting phenix.real_space_refine
on Tue Feb 11 03:00:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qvw_18674/02_2025/8qvw_18674.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      18      5.16       5
     C    2484      2.51       5
     N     680      2.21       5
     O     736      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3918
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 451
          Classifications: {'peptide': 56}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 47}
    Chain: "B"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3467
          Classifications: {'peptide': 436}
          Link IDs: {'PTRANS': 10, 'TRANS': 425}
          Chain breaks: 2
  Time building chain proxies: 2.57, per 1000 atoms: 0.66
  Number of scatterers: 3918
  At special positions: 0
  Unit cell: (115.14, 72.96, 70.68, 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      18     16.00
     O     736      8.00
     N     680      7.00
     C    2484      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: 0.88
  Conformation dependent library (CDL) restraints added in 509.3 milliseconds
  

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      81.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 553 through 557
    Processing helix  chain 'A' and resid 564 through 568
    Processing helix  chain 'A' and resid 592 through 597
      removed outlier: 3.678A  pdb=" N   LEU A 595 " --> pdb=" O   ASP A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.936A  pdb=" N   LEU A 607 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 25
    Processing helix  chain 'B' and resid 27 through 41
    Processing helix  chain 'B' and resid 44 through 58
    Processing helix  chain 'B' and resid 60 through 76
      removed outlier: 5.121A  pdb=" N   LYS B  73 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   VAL B  74 " --> pdb=" O   THR B  70 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA B  76 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 91
    Processing helix  chain 'B' and resid 93 through 103
      removed outlier: 3.779A  pdb=" N   LYS B  99 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 122
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 143 through 162
    Processing helix  chain 'B' and resid 176 through 190
    Processing helix  chain 'B' and resid 192 through 211
      removed outlier: 3.513A  pdb=" N   MET B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS B 197 " --> pdb=" O   ASN B 193 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER B 211 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 239
      removed outlier: 3.587A  pdb=" N   ILE B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 256
      removed outlier: 3.557A  pdb=" N   LYS B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 275
    Processing helix  chain 'B' and resid 278 through 290
      removed outlier: 3.607A  pdb=" N   LYS B 284 " --> pdb=" O   PHE B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 298
    Processing helix  chain 'B' and resid 299 through 317
    Processing helix  chain 'B' and resid 320 through 333
      removed outlier: 3.599A  pdb=" N   GLN B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
    Processing helix  chain 'B' and resid 354 through 368
      removed outlier: 3.756A  pdb=" N   GLU B 359 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 383
      removed outlier: 3.889A  pdb=" N   ILE B 375 " --> pdb=" O   ASN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 398
    Processing helix  chain 'B' and resid 405 through 419
      removed outlier: 3.619A  pdb=" N   GLU B 419 " --> pdb=" O   MET B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 440
    Processing helix  chain 'B' and resid 443 through 460

    271 hydrogen bonds defined for protein.
    792 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: 0.99

  Time building geometry restraints manager: 1.02 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: 1306
        1.34 -     1.46: 560
        1.46 -     1.58: 2093
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3983
  Sorted by residual:
  bond pdb=" CB  PHE A 561 "
       pdb=" CG  PHE A 561 "
    ideal  model  delta    sigma   weight residual
    1.502  1.531 -0.029 2.30e-02 1.89e+03 1.58e+00
  bond pdb=" CB  ASN B 318 "
       pdb=" CG  ASN B 318 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.56e+00
  bond pdb=" CA  ASN B 318 "
       pdb=" CB  ASN B 318 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.69e-02 3.50e+03 1.14e+00
  bond pdb=" CB  GLU B 427 "
       pdb=" CG  GLU B 427 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.07e+00
  bond pdb=" CA  GLU B 427 "
       pdb=" CB  GLU B 427 "
    ideal  model  delta    sigma   weight residual
    1.528  1.544 -0.015 1.59e-02 3.96e+03 9.26e-01
  ... (remaining 3978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 5264
        1.79 -     3.57: 102
        3.57 -     5.36: 10
        5.36 -     7.14: 3
        7.14 -     8.93: 4
  Bond angle restraints: 5383
  Sorted by residual:
  angle pdb=" C   ALA B  76 "
        pdb=" CA  ALA B  76 "
        pdb=" CB  ALA B  76 "
      ideal   model   delta    sigma   weight residual
     115.79  109.95    5.84 1.19e+00 7.06e-01 2.41e+01
  angle pdb=" CA  GLU B 427 "
        pdb=" CB  GLU B 427 "
        pdb=" CG  GLU B 427 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" C   LEU A 563 "
        pdb=" N   ASP A 564 "
        pdb=" CA  ASP A 564 "
      ideal   model   delta    sigma   weight residual
     121.80  129.42   -7.62 2.44e+00 1.68e-01 9.76e+00
  angle pdb=" CA  LEU B 402 "
        pdb=" CB  LEU B 402 "
        pdb=" CG  LEU B 402 "
      ideal   model   delta    sigma   weight residual
     116.30  125.23   -8.93 3.50e+00 8.16e-02 6.50e+00
  angle pdb=" N   GLN B 353 "
        pdb=" CA  GLN B 353 "
        pdb=" C   GLN B 353 "
      ideal   model   delta    sigma   weight residual
     109.71  106.19    3.52 1.41e+00 5.03e-01 6.24e+00
  ... (remaining 5378 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 2081
       17.63 -    35.26: 288
       35.26 -    52.89: 74
       52.89 -    70.51: 15
       70.51 -    88.14: 9
  Dihedral angle restraints: 2467
    sinusoidal: 1008
      harmonic: 1459
  Sorted by residual:
  dihedral pdb=" CA  ASN B 388 "
           pdb=" CB  ASN B 388 "
           pdb=" CG  ASN B 388 "
           pdb=" OD1 ASN B 388 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -164.64   74.64     2      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  LYS B 383 "
           pdb=" C   LYS B 383 "
           pdb=" N   ILE B 384 "
           pdb=" CA  ILE B 384 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.37   16.63     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  GLU B 351 "
           pdb=" C   GLU B 351 "
           pdb=" N   LYS B 352 "
           pdb=" CA  LYS B 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 2464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 445
       0.039 -    0.078: 142
       0.078 -    0.116: 30
       0.116 -    0.155: 2
       0.155 -    0.194: 1
  Chirality restraints: 620
  Sorted by residual:
  chirality pdb=" CG  LEU B 402 "
            pdb=" CB  LEU B 402 "
            pdb=" CD1 LEU B 402 "
            pdb=" CD2 LEU B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.39e-01
  chirality pdb=" CA  ASN B 318 "
            pdb=" N   ASN B 318 "
            pdb=" C   ASN B 318 "
            pdb=" CB  ASN B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ASP A 564 "
            pdb=" N   ASP A 564 "
            pdb=" C   ASP A 564 "
            pdb=" CB  ASP A 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 617 not shown)

  Planarity restraints: 694
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 561 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.84e+00
        pdb=" C   PHE A 561 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PHE A 561 "    0.013 2.00e-02 2.50e+03
        pdb=" N   CYS A 562 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 598 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.09e+00
        pdb=" C   VAL A 598 "    0.025 2.00e-02 2.50e+03
        pdb=" O   VAL A 598 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A 599 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  21 "    0.010 2.00e-02 2.50e+03   8.27e-03 1.37e+00
        pdb=" CG  TYR B  21 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  21 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  21 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  21 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  21 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  21 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  21 "    0.000 2.00e-02 2.50e+03
  ... (remaining 691 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 97
        2.70 -     3.25: 4250
        3.25 -     3.80: 6680
        3.80 -     4.35: 8170
        4.35 -     4.90: 13230
  Nonbonded interactions: 32427
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 406 "
            pdb=" OG  SER B 410 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" N   GLU B 146 "
            pdb=" OE1 GLU B 146 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   ASN B 278 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASP B 141 "
            pdb=" NH1 ARG B 147 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   LEU B 313 "
            pdb=" OG1 THR B 317 "
     model   vdw
     2.299 3.040
  ... (remaining 32422 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:11.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
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   0.036   3983  Z= 0.179
  Angle     :  0.601   8.925   5383  Z= 0.318
  Chirality :  0.038   0.194    620
  Planarity :  0.003   0.027    694
  Dihedral  : 18.024  88.143   1511
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 25.12 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.40), residues: 484
  helix:  1.20 (0.27), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.20 (0.66), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.011   0.001   PHE A 561 
 TYR   0.020   0.001   TYR B  21 
 ARG   0.006   0.001   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 TYR cc_start: 0.6012 (t80) cc_final: 0.4898 (t80)
REVERT: B  408 MET cc_start: 0.7442 (ttt) cc_final: 0.7130 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.9939
  time to fit residues: 67.3949
Evaluate side-chains
  59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0370
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
B  78 ASN
B  92 ASN
B 274 ASN
B 278 ASN
B 302 GLN
B 304 GLN
B 309 ASN
B 322 GLN
B 333 GLN
B 347 GLN
B 353 GLN
B 439 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.148304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.120404 restraints weight = 7392.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.74
r_work: 0.3578 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3983  Z= 0.186
  Angle     :  0.568   7.435   5383  Z= 0.294
  Chirality :  0.039   0.135    620
  Planarity :  0.003   0.028    694
  Dihedral  :  3.995  16.525    520
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.35 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.39), residues: 484
  helix:  1.36 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.01 (0.66), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 161 
 HIS   0.002   0.001   HIS B 439 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.016   0.001   TYR B 132 
 ARG   0.003   0.000   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 TYR cc_start: 0.5073 (t80) cc_final: 0.4811 (t80)
REVERT: B   23 GLN cc_start: 0.7660 (pt0) cc_final: 0.7424 (pt0)
REVERT: B  366 ASP cc_start: 0.8060 (m-30) cc_final: 0.7849 (m-30)
REVERT: B  388 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8039 (t0)
REVERT: B  408 MET cc_start: 0.7232 (ttt) cc_final: 0.6870 (ttt)
REVERT: B  427 GLU cc_start: 0.8461 (pp20) cc_final: 0.8051 (pp20)
  outliers start: 12
  outliers final: 3
  residues processed: 71
  average time/residue: 1.0358
  time to fit residues: 76.6211
Evaluate side-chains
  59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 347 GLN
B 353 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.146521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.118377 restraints weight = 7389.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.74
r_work: 0.3556 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3983  Z= 0.217
  Angle     :  0.575   7.861   5383  Z= 0.295
  Chirality :  0.039   0.137    620
  Planarity :  0.003   0.022    694
  Dihedral  :  3.953  16.008    520
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 26.50 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.39), residues: 484
  helix:  1.33 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.10 (0.65), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.013   0.001   TYR B  21 
 ARG   0.004   0.000   ARG B  29 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7675 (pt0) cc_final: 0.7453 (pt0)
REVERT: B   29 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7265 (ttt-90)
REVERT: B   42 LYS cc_start: 0.8167 (tppt) cc_final: 0.7934 (mmtm)
REVERT: B  222 GLN cc_start: 0.6794 (mp10) cc_final: 0.6470 (mp10)
REVERT: B  366 ASP cc_start: 0.8091 (m-30) cc_final: 0.7864 (m-30)
REVERT: B  388 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (t0)
REVERT: B  427 GLU cc_start: 0.8375 (pp20) cc_final: 0.8115 (pp20)
  outliers start: 15
  outliers final: 4
  residues processed: 70
  average time/residue: 0.9461
  time to fit residues: 69.2507
Evaluate side-chains
  60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    0.3980
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    0.3980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
B 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.143473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.115193 restraints weight = 7358.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.68
r_work: 0.3507 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3983  Z= 0.306
  Angle     :  0.601   7.715   5383  Z= 0.309
  Chirality :  0.041   0.146    620
  Planarity :  0.003   0.032    694
  Dihedral  :  4.067  16.987    520
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 24.65 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.38), residues: 484
  helix:  0.87 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.05 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.014   0.002   PHE B 429 
 TYR   0.014   0.002   TYR B  21 
 ARG   0.006   0.001   ARG B 133 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7258 (mt) cc_final: 0.6647 (mt)
REVERT: B   23 GLN cc_start: 0.7851 (pt0) cc_final: 0.7624 (pt0)
REVERT: B   29 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7085 (ttt-90)
REVERT: B   42 LYS cc_start: 0.8126 (tppt) cc_final: 0.7839 (mmtm)
REVERT: B  178 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (tt)
REVERT: B  208 ARG cc_start: 0.8247 (mmp80) cc_final: 0.7823 (mpp-170)
REVERT: B  424 SER cc_start: 0.6990 (OUTLIER) cc_final: 0.6784 (p)
REVERT: B  427 GLU cc_start: 0.8547 (pp20) cc_final: 0.8136 (pp20)
  outliers start: 23
  outliers final: 8
  residues processed: 78
  average time/residue: 0.9873
  time to fit residues: 80.2876
Evaluate side-chains
  66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  458 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 331 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.144486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.116312 restraints weight = 7659.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.75
r_work: 0.3520 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3983  Z= 0.246
  Angle     :  0.608   8.124   5383  Z= 0.311
  Chirality :  0.041   0.162    620
  Planarity :  0.003   0.037    694
  Dihedral  :  4.059  16.294    520
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.35 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.38), residues: 484
  helix:  0.88 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.05 (0.68), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 404 
 PHE   0.014   0.001   PHE B 429 
 TYR   0.011   0.001   TYR B  86 
 ARG   0.009   0.001   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7260 (mt) cc_final: 0.6824 (mt)
REVERT: B   23 GLN cc_start: 0.7813 (pt0) cc_final: 0.7558 (pt0)
REVERT: B   29 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7155 (ttt180)
REVERT: B  178 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (tt)
REVERT: B  208 ARG cc_start: 0.8229 (mmp80) cc_final: 0.7755 (mpp-170)
REVERT: B  222 GLN cc_start: 0.6951 (mm-40) cc_final: 0.5459 (mp10)
REVERT: B  382 LEU cc_start: 0.8237 (mm) cc_final: 0.7946 (mm)
REVERT: B  427 GLU cc_start: 0.8517 (pp20) cc_final: 0.8306 (pp20)
  outliers start: 18
  outliers final: 8
  residues processed: 71
  average time/residue: 0.8929
  time to fit residues: 66.3266
Evaluate side-chains
  65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  395 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    7.9990
   chunk 20 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.145914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.118012 restraints weight = 7326.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.67
r_work: 0.3550 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3983  Z= 0.203
  Angle     :  0.604   9.880   5383  Z= 0.306
  Chirality :  0.039   0.136    620
  Planarity :  0.003   0.028    694
  Dihedral  :  4.010  15.237    520
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 27.19 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.39), residues: 484
  helix:  0.93 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.01 (0.68), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 404 
 PHE   0.015   0.001   PHE B 429 
 TYR   0.011   0.001   TYR B  21 
 ARG   0.005   0.001   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7224 (mt) cc_final: 0.6525 (mp)
REVERT: B   23 GLN cc_start: 0.7766 (pt0) cc_final: 0.7502 (pt0)
REVERT: B   29 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7123 (ttt180)
REVERT: B  178 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (tt)
REVERT: B  208 ARG cc_start: 0.8168 (mmp80) cc_final: 0.7688 (mpp-170)
REVERT: B  222 GLN cc_start: 0.6935 (mm-40) cc_final: 0.5426 (mp10)
REVERT: B  382 LEU cc_start: 0.8206 (mm) cc_final: 0.7911 (mm)
REVERT: B  427 GLU cc_start: 0.8554 (pp20) cc_final: 0.8102 (pp20)
  outliers start: 17
  outliers final: 9
  residues processed: 72
  average time/residue: 0.8951
  time to fit residues: 67.4318
Evaluate side-chains
  66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.147003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.119045 restraints weight = 7406.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.73
r_work: 0.3567 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3983  Z= 0.183
  Angle     :  0.609   9.777   5383  Z= 0.310
  Chirality :  0.039   0.140    620
  Planarity :  0.003   0.023    694
  Dihedral  :  3.988  17.686    520
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 27.42 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.39), residues: 484
  helix:  0.95 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.17 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.013   0.001   PHE B 429 
 TYR   0.007   0.001   TYR B 132 
 ARG   0.005   0.000   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7192 (mt) cc_final: 0.6505 (mp)
REVERT: B   23 GLN cc_start: 0.7737 (pt0) cc_final: 0.7465 (pt0)
REVERT: B   29 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7050 (ttp80)
REVERT: B  178 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8165 (tt)
REVERT: B  208 ARG cc_start: 0.8204 (mmp80) cc_final: 0.7761 (mpp-170)
REVERT: B  222 GLN cc_start: 0.6947 (mm-40) cc_final: 0.5412 (mp10)
REVERT: B  382 LEU cc_start: 0.8168 (mm) cc_final: 0.7872 (mm)
REVERT: B  415 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (ttm)
  outliers start: 17
  outliers final: 11
  residues processed: 69
  average time/residue: 0.8107
  time to fit residues: 58.8141
Evaluate side-chains
  66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0050
   chunk 34 optimal weight:    0.3980
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 42 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.148079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.120327 restraints weight = 7278.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.61
r_work: 0.3589 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3983  Z= 0.176
  Angle     :  0.613   9.815   5383  Z= 0.313
  Chirality :  0.039   0.136    620
  Planarity :  0.003   0.022    694
  Dihedral  :  3.960  17.906    520
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 27.42 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.39), residues: 484
  helix:  1.01 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.21 (0.69), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 161 
 HIS   0.003   0.000   HIS B 404 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.013   0.001   TYR B  21 
 ARG   0.004   0.000   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7198 (mt) cc_final: 0.6505 (mp)
REVERT: B   23 GLN cc_start: 0.7675 (pt0) cc_final: 0.7376 (pt0)
REVERT: B   29 ARG cc_start: 0.7450 (mtt180) cc_final: 0.7010 (ttp80)
REVERT: B  178 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: B  208 ARG cc_start: 0.8200 (mmp80) cc_final: 0.7932 (mmp80)
REVERT: B  210 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5615 (pt)
REVERT: B  222 GLN cc_start: 0.6921 (mm-40) cc_final: 0.5356 (mp10)
REVERT: B  408 MET cc_start: 0.7171 (ttt) cc_final: 0.6922 (ptm)
REVERT: B  415 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8158 (ttm)
  outliers start: 18
  outliers final: 6
  residues processed: 69
  average time/residue: 0.8484
  time to fit residues: 61.3327
Evaluate side-chains
  65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0470
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.148639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.120933 restraints weight = 7308.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.65
r_work: 0.3594 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3983  Z= 0.175
  Angle     :  0.634  11.129   5383  Z= 0.319
  Chirality :  0.038   0.135    620
  Planarity :  0.003   0.021    694
  Dihedral  :  3.917  18.138    520
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 29.26 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.39), residues: 484
  helix:  1.13 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.26 (0.70), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 161 
 HIS   0.003   0.000   HIS B 404 
 PHE   0.013   0.001   PHE B 429 
 TYR   0.021   0.001   TYR B  21 
 ARG   0.004   0.000   ARG B 133 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8792 (tp) cc_final: 0.8559 (tp)
REVERT: A  607 LEU cc_start: 0.7231 (mt) cc_final: 0.6550 (mp)
REVERT: B   21 TYR cc_start: 0.4905 (t80) cc_final: 0.3400 (t80)
REVERT: B   23 GLN cc_start: 0.7666 (pt0) cc_final: 0.7368 (pt0)
REVERT: B  178 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (tt)
REVERT: B  208 ARG cc_start: 0.8186 (mmp80) cc_final: 0.7929 (mmp80)
REVERT: B  210 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5632 (pt)
REVERT: B  222 GLN cc_start: 0.6886 (mm-40) cc_final: 0.5298 (mp10)
REVERT: B  366 ASP cc_start: 0.8162 (m-30) cc_final: 0.7932 (m-30)
REVERT: B  415 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8221 (ttm)
  outliers start: 12
  outliers final: 8
  residues processed: 69
  average time/residue: 0.8320
  time to fit residues: 60.3376
Evaluate side-chains
  70 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 331 GLN
B 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.145006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.116817 restraints weight = 7382.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.61
r_work: 0.3534 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   3983  Z= 0.293
  Angle     :  0.686  10.993   5383  Z= 0.348
  Chirality :  0.042   0.160    620
  Planarity :  0.003   0.024    694
  Dihedral  :  4.034  18.253    520
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 29.26 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.38), residues: 484
  helix:  0.88 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.03 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.012   0.002   PHE B 429 
 TYR   0.012   0.002   TYR B  86 
 ARG   0.003   0.001   ARG A 557 

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

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

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  968 Ramachandran restraints generated.
    484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7328 (mt) cc_final: 0.6627 (mp)
REVERT: B   29 ARG cc_start: 0.7241 (mpp80) cc_final: 0.6603 (tmm160)
REVERT: B  178 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (tt)
REVERT: B  208 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7787 (mpp-170)
REVERT: B  210 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5667 (pt)
REVERT: B  222 GLN cc_start: 0.7012 (mm-40) cc_final: 0.5373 (mp10)
REVERT: B  382 LEU cc_start: 0.8336 (mm) cc_final: 0.8035 (mm)
REVERT: B  408 MET cc_start: 0.7100 (ttt) cc_final: 0.6807 (ptm)
  outliers start: 14
  outliers final: 9
  residues processed: 64
  average time/residue: 0.8932
  time to fit residues: 59.8614
Evaluate side-chains
  64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 ASP
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  354 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0050
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0770
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.2752

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

Flipped N/Q/H residues before XYZ refinement:
B 331 GLN
B 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.148995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.121413 restraints weight = 7177.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.57
r_work: 0.3605 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3983  Z= 0.188
  Angle     :  0.665  11.444   5383  Z= 0.334
  Chirality :  0.039   0.143    620
  Planarity :  0.003   0.021    694
  Dihedral  :  3.946  18.102    520
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 30.65 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.39), residues: 484
  helix:  1.06 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.19 (0.70), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 404 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.013   0.001   TYR B  21 
 ARG   0.004   0.000   ARG B 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2790.87 seconds
wall clock time: 50 minutes 17.50 seconds (3017.50 seconds total)