Starting phenix.real_space_refine
on Wed Mar  5 22:14:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qvw_18674/03_2025/8qvw_18674.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qvw_18674/03_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_18674/03_2025/8qvw_18674.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qvw_18674/03_2025/8qvw_18674.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qvw_18674/03_2025/8qvw_18674.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qvw_18674/03_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-5624/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: 2.81, per 1000 atoms: 0.72
  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: 0.92
  Conformation dependent library (CDL) restraints added in 467.3 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: 0.37
  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: 1.05

  Time building geometry restraints manager: 1.12 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:             0.380
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.590
  Find NCS groups from input model:        0.040
  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:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.940
-------------------------------------------------------------------------------
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  : 0.457 
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: 0.9497
  time to fit residues: 64.4531
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  : 0.485 
-------------------------------------------------------------------------------
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 = 33)----------------|
| 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: 0.3577 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
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  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 TYR cc_start: 0.5071 (t80) cc_final: 0.4805 (t80)
REVERT: B   23 GLN cc_start: 0.7657 (pt0) cc_final: 0.7420 (pt0)
REVERT: B  366 ASP cc_start: 0.8061 (m-30) cc_final: 0.7854 (m-30)
REVERT: B  388 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8038 (t0)
REVERT: B  408 MET cc_start: 0.7218 (ttt) cc_final: 0.6855 (ttt)
REVERT: B  427 GLU cc_start: 0.8459 (pp20) cc_final: 0.8049 (pp20)
  outliers start: 12
  outliers final: 3
  residues processed: 71
  average time/residue: 1.0333
  time to fit residues: 76.2781
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  : 0.442 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.145834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.117551 restraints weight = 7397.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.74
r_work: 0.3542 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3983  Z= 0.237
  Angle     :  0.582   8.112   5383  Z= 0.300
  Chirality :  0.040   0.139    620
  Planarity :  0.003   0.022    694
  Dihedral  :  3.973  16.301    520
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.81 %
    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:  1.37 (0.39), residues: 484
  helix:  1.27 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.12 (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   0.012   0.001   PHE B 429 
 TYR   0.015   0.001   TYR B  21 
 ARG   0.003   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
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7686 (pt0) cc_final: 0.7457 (pt0)
REVERT: B   29 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7345 (ttt-90)
REVERT: B   42 LYS cc_start: 0.8190 (tppt) cc_final: 0.7934 (mmtm)
REVERT: B  222 GLN cc_start: 0.6804 (mp10) cc_final: 0.6484 (mp10)
REVERT: B  366 ASP cc_start: 0.8079 (m-30) cc_final: 0.7829 (m-30)
REVERT: B  388 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8175 (t0)
REVERT: B  427 GLU cc_start: 0.8390 (pp20) cc_final: 0.8126 (pp20)
  outliers start: 16
  outliers final: 4
  residues processed: 71
  average time/residue: 0.8970
  time to fit residues: 66.5617
Evaluate side-chains
  63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.144899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.116726 restraints weight = 7349.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.68
r_work: 0.3532 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3983  Z= 0.250
  Angle     :  0.578   8.101   5383  Z= 0.297
  Chirality :  0.040   0.135    620
  Planarity :  0.003   0.033    694
  Dihedral  :  4.003  16.408    520
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 25.35 %
    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:  1.10 (0.39), residues: 484
  helix:  1.00 (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   0.015   0.002   PHE B 429 
 TYR   0.013   0.001   TYR B  21 
 ARG   0.007   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
  83 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7298 (mt) cc_final: 0.6892 (mt)
REVERT: B   23 GLN cc_start: 0.7836 (pt0) cc_final: 0.7610 (pt0)
REVERT: B   29 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7053 (ttt180)
REVERT: B   42 LYS cc_start: 0.8099 (tppt) cc_final: 0.7835 (mmtm)
REVERT: B  178 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (tt)
REVERT: B  427 GLU cc_start: 0.8528 (pp20) cc_final: 0.8096 (pp20)
  outliers start: 20
  outliers final: 7
  residues processed: 76
  average time/residue: 1.0600
  time to fit residues: 83.8306
Evaluate side-chains
  66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
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
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:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 347 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.145707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.117444 restraints weight = 7587.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.74
r_work: 0.3544 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1854

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= 0.219
  Angle     :  0.599   8.079   5383  Z= 0.306
  Chirality :  0.040   0.143    620
  Planarity :  0.003   0.034    694
  Dihedral  :  4.005  15.679    520
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  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:  1.12 (0.38), residues: 484
  helix:  1.02 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.05 (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   0.014   0.001   PHE B 429 
 TYR   0.009   0.001   TYR B  86 
 ARG   0.008   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
  76 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7251 (mt) cc_final: 0.6812 (mt)
REVERT: B   23 GLN cc_start: 0.7824 (pt0) cc_final: 0.7578 (pt0)
REVERT: B   29 ARG cc_start: 0.7441 (mtt180) cc_final: 0.7134 (ttt180)
REVERT: B   42 LYS cc_start: 0.8177 (tppt) cc_final: 0.7947 (mmtm)
REVERT: B  178 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (tt)
REVERT: B  222 GLN cc_start: 0.7049 (mm-40) cc_final: 0.5698 (mp10)
REVERT: B  427 GLU cc_start: 0.8511 (pp20) cc_final: 0.8299 (pp20)
  outliers start: 15
  outliers final: 6
  residues processed: 70
  average time/residue: 0.9726
  time to fit residues: 71.4799
Evaluate side-chains
  64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.145257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.117254 restraints weight = 7413.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.69
r_work: 0.3543 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3983  Z= 0.226
  Angle     :  0.609   9.363   5383  Z= 0.309
  Chirality :  0.040   0.135    620
  Planarity :  0.003   0.022    694
  Dihedral  :  4.010  15.285    520
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.73 %
    Favored  : 69.59 %
  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:  1.02 (0.39), residues: 484
  helix:  0.92 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop :  0.12 (0.69), residues: 101

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   0.012   0.001   PHE B 429 
 TYR   0.010   0.001   TYR B  86 
 ARG   0.005   0.001   ARG B 133 

*********************** 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: 16
    poor density    : 61
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  570 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8330 (mmtt)
REVERT: A  607 LEU cc_start: 0.7276 (mt) cc_final: 0.6586 (mp)
REVERT: B   23 GLN cc_start: 0.7782 (pt0) cc_final: 0.7517 (pt0)
REVERT: B   29 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7162 (ttt180)
REVERT: B   35 ASN cc_start: 0.7921 (p0) cc_final: 0.7694 (p0)
REVERT: B  178 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (tt)
REVERT: B  222 GLN cc_start: 0.7029 (mm-40) cc_final: 0.5549 (mp10)
REVERT: B  427 GLU cc_start: 0.8579 (pp20) cc_final: 0.8160 (pp20)
  outliers start: 16
  outliers final: 9
  residues processed: 72
  average time/residue: 0.9396
  time to fit residues: 70.7032
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  : 0.473 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  458 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 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 = 0.4038 r_free = 0.4038 target = 0.142904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.114337 restraints weight = 7402.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.67
r_work: 0.3492 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   3983  Z= 0.343
  Angle     :  0.664   8.717   5383  Z= 0.340
  Chirality :  0.042   0.134    620
  Planarity :  0.003   0.034    694
  Dihedral  :  4.146  16.273    520
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 26.73 %
    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:  0.59 (0.38), residues: 484
  helix:  0.67 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.26 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 161 
 HIS   0.004   0.001   HIS B 404 
 PHE   0.011   0.002   PHE B 429 
 TYR   0.017   0.002   TYR B  21 
 ARG   0.004   0.001   ARG B 208 

*********************** 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
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  570 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8343 (mmtt)
REVERT: A  607 LEU cc_start: 0.7524 (mt) cc_final: 0.6883 (mt)
REVERT: B   21 TYR cc_start: 0.5321 (t80) cc_final: 0.3552 (t80)
REVERT: B   23 GLN cc_start: 0.7742 (pt0) cc_final: 0.7441 (pt0)
REVERT: B   35 ASN cc_start: 0.7941 (p0) cc_final: 0.7729 (p0)
REVERT: B  178 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: B  222 GLN cc_start: 0.7113 (mm-40) cc_final: 0.5588 (mp10)
REVERT: B  427 GLU cc_start: 0.8503 (pp20) cc_final: 0.8289 (pp20)
  outliers start: 20
  outliers final: 9
  residues processed: 72
  average time/residue: 0.9232
  time to fit residues: 69.4551
Evaluate side-chains
  63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 ASP
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
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  458 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 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 = 0.4064 r_free = 0.4064 target = 0.144975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.117240 restraints weight = 7288.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.59
r_work: 0.3544 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3983  Z= 0.214
  Angle     :  0.655  10.430   5383  Z= 0.325
  Chirality :  0.040   0.141    620
  Planarity :  0.003   0.019    694
  Dihedral  :  4.059  15.455    520
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.11 %
    Favored  : 68.20 %
  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:  0.84 (0.39), residues: 484
  helix:  0.82 (0.26), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.07 (0.69), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 404 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.010   0.001   TYR B  86 
 ARG   0.005   0.001   ARG B 208 

*********************** 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
  77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8334 (mmtt)
REVERT: A  607 LEU cc_start: 0.7493 (mt) cc_final: 0.6814 (mt)
REVERT: B   23 GLN cc_start: 0.8002 (pt0) cc_final: 0.7779 (pt0)
REVERT: B   29 ARG cc_start: 0.7264 (mpp80) cc_final: 0.6756 (ttp80)
REVERT: B  178 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8231 (tt)
REVERT: B  208 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7876 (mmp80)
REVERT: B  210 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5667 (pt)
REVERT: B  222 GLN cc_start: 0.7075 (mm-40) cc_final: 0.5548 (mp10)
REVERT: B  382 LEU cc_start: 0.8282 (mm) cc_final: 0.8031 (mm)
REVERT: B  427 GLU cc_start: 0.8489 (pp20) cc_final: 0.8162 (pp20)
  outliers start: 16
  outliers final: 9
  residues processed: 73
  average time/residue: 0.8274
  time to fit residues: 63.4082
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  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 LEU
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  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
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  458 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.145707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117776 restraints weight = 7340.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.66
r_work: 0.3554 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3983  Z= 0.206
  Angle     :  0.660  11.115   5383  Z= 0.329
  Chirality :  0.040   0.159    620
  Planarity :  0.003   0.024    694
  Dihedral  :  4.025  14.678    520
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.57 %
    Favored  : 67.74 %
  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 (0.39), residues: 484
  helix:  0.88 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.07 (0.70), 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   0.001   PHE B 429 
 TYR   0.008   0.001   TYR B  86 
 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: 16
    poor density    : 59
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8740 (tp) cc_final: 0.8540 (tp)
REVERT: A  607 LEU cc_start: 0.7418 (mt) cc_final: 0.6745 (mt)
REVERT: B   23 GLN cc_start: 0.7760 (pt0) cc_final: 0.7475 (pt0)
REVERT: B   29 ARG cc_start: 0.7209 (mpp80) cc_final: 0.6754 (ttp80)
REVERT: B  178 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8180 (tt)
REVERT: B  196 MET cc_start: 0.8111 (mmm) cc_final: 0.7863 (tpt)
REVERT: B  208 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7812 (mmp80)
REVERT: B  210 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5650 (pt)
REVERT: B  222 GLN cc_start: 0.6957 (mm-40) cc_final: 0.5386 (mp10)
REVERT: B  408 MET cc_start: 0.7140 (ttt) cc_final: 0.6903 (ptm)
  outliers start: 16
  outliers final: 8
  residues processed: 72
  average time/residue: 0.8297
  time to fit residues: 62.7156
Evaluate side-chains
  67 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   98 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.145840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117958 restraints weight = 7374.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.65
r_work: 0.3559 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3983  Z= 0.220
  Angle     :  0.696  11.376   5383  Z= 0.344
  Chirality :  0.040   0.155    620
  Planarity :  0.003   0.025    694
  Dihedral  :  4.011  14.397    520
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 29.49 %
    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:  1.00 (0.39), residues: 484
  helix:  0.97 (0.26), residues: 377
  sheet:  None (None), residues: 0
  loop : -0.14 (0.68), residues: 107

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   0.014   0.001   PHE B 429 
 TYR   0.008   0.001   TYR B  86 
 ARG   0.004   0.000   ARG B 133 

********************** 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
  71 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8760 (tp) cc_final: 0.8556 (tp)
REVERT: A  607 LEU cc_start: 0.7407 (mt) cc_final: 0.6738 (mt)
REVERT: B   23 GLN cc_start: 0.7715 (pt0) cc_final: 0.7503 (pt0)
REVERT: B   29 ARG cc_start: 0.7164 (mpp80) cc_final: 0.6744 (ttp80)
REVERT: B  178 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8183 (tt)
REVERT: B  208 ARG cc_start: 0.8119 (mmp80) cc_final: 0.7805 (mmp80)
REVERT: B  210 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5654 (pt)
REVERT: B  222 GLN cc_start: 0.6940 (mm-40) cc_final: 0.5367 (mp10)
REVERT: B  382 LEU cc_start: 0.8293 (mm) cc_final: 0.8004 (mm)
REVERT: B  408 MET cc_start: 0.7142 (ttt) cc_final: 0.6930 (ptm)
  outliers start: 13
  outliers final: 9
  residues processed: 67
  average time/residue: 0.8466
  time to fit residues: 59.5032
Evaluate side-chains
  68 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   98 LEU
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  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
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 6 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.146170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.118180 restraints weight = 7257.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.65
r_work: 0.3562 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2360

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= 0.223
  Angle     :  0.698  11.289   5383  Z= 0.345
  Chirality :  0.040   0.154    620
  Planarity :  0.003   0.025    694
  Dihedral  :  4.009  14.293    520
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 29.72 %
    Favored  : 67.28 %
  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:  0.98 (0.39), residues: 484
  helix:  0.90 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.04 (0.70), 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   0.009   0.001   TYR B  86 
 ARG   0.004   0.001   ARG B 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2883.77 seconds
wall clock time: 50 minutes 10.08 seconds (3010.08 seconds total)