Starting phenix.real_space_refine
on Fri Aug 22 14:08:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qvw_18674/08_2025/8qvw_18674.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qvw_18674/08_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_18674/08_2025/8qvw_18674.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qvw_18674/08_2025/8qvw_18674.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qvw_18674/08_2025/8qvw_18674.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qvw_18674/08_2025/8qvw_18674.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 0.85, per 1000 atoms: 0.22
  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: 0.20
  Conformation dependent library (CDL) restraints added in 93.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.13
  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: 0.70

  Time building geometry restraints manager: 0.29 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.900
  Find NCS groups from input model:        0.020
  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:7.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
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= 0.129
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (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
 ARG   0.006   0.001   ARG A 557 
 TYR   0.020   0.001   TYR B  21 
 PHE   0.011   0.001   PHE A 561 
 TRP   0.007   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3983)
  covalent geometry    : angle       0.60071 ( 5383)
  hydrogen bonds       : bond        0.12746 (  271)
  hydrogen bonds       : angle       5.05682 (  792)

*********************** 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  : 0.151 
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: 0.4256
  time to fit residues: 28.6586
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  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 362 GLN
B 439 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.148237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.120197 restraints weight = 7453.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.77
r_work: 0.3576 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3983  Z= 0.132
  Angle     :  0.569   7.436   5383  Z= 0.295
  Chirality :  0.039   0.135    620
  Planarity :  0.003   0.028    694
  Dihedral  :  3.985  16.514    520
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 25.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.39), residues: 484
  helix:  1.37 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.01 (0.66), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.016   0.001   TYR B 132 
 PHE   0.010   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.002   0.001   HIS B 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3983)
  covalent geometry    : angle       0.56900 ( 5383)
  hydrogen bonds       : bond        0.03662 (  271)
  hydrogen bonds       : angle       4.09802 (  792)

*********************** 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
  78 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 TYR cc_start: 0.5078 (t80) cc_final: 0.4818 (t80)
REVERT: B   23 GLN cc_start: 0.7646 (pt0) cc_final: 0.7411 (pt0)
REVERT: B  366 ASP cc_start: 0.8084 (m-30) cc_final: 0.7857 (m-30)
REVERT: B  388 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8059 (t0)
REVERT: B  408 MET cc_start: 0.7205 (ttt) cc_final: 0.6853 (ttt)
REVERT: B  427 GLU cc_start: 0.8456 (pp20) cc_final: 0.8051 (pp20)
  outliers start: 13
  outliers final: 3
  residues processed: 71
  average time/residue: 0.4790
  time to fit residues: 35.1546
Evaluate side-chains
  60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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 6 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.1980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.148633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.120416 restraints weight = 7488.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.80
r_work: 0.3585 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3983  Z= 0.121
  Angle     :  0.568   8.120   5383  Z= 0.290
  Chirality :  0.038   0.140    620
  Planarity :  0.003   0.020    694
  Dihedral  :  3.913  15.308    520
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.39), residues: 484
  helix:  1.42 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.08 (0.65), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  29 
 TYR   0.014   0.001   TYR B  21 
 PHE   0.012   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3983)
  covalent geometry    : angle       0.56753 ( 5383)
  hydrogen bonds       : bond        0.03329 (  271)
  hydrogen bonds       : angle       3.92920 (  792)

*********************** 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
  69 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7632 (pt0) cc_final: 0.7387 (pt0)
REVERT: B   42 LYS cc_start: 0.8140 (tppt) cc_final: 0.7936 (mmtm)
REVERT: B  196 MET cc_start: 0.8013 (mmm) cc_final: 0.7793 (tpt)
REVERT: B  366 ASP cc_start: 0.8074 (m-30) cc_final: 0.7822 (m-30)
REVERT: B  388 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (t0)
REVERT: B  408 MET cc_start: 0.7156 (ttt) cc_final: 0.6833 (ttt)
REVERT: B  427 GLU cc_start: 0.8429 (pp20) cc_final: 0.8167 (pp20)
  outliers start: 12
  outliers final: 4
  residues processed: 64
  average time/residue: 0.4314
  time to fit residues: 28.6911
Evaluate side-chains
  57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
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 43 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   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  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.146933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.118764 restraints weight = 7398.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.75
r_work: 0.3566 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3983  Z= 0.133
  Angle     :  0.572   7.310   5383  Z= 0.289
  Chirality :  0.039   0.137    620
  Planarity :  0.003   0.020    694
  Dihedral  :  3.918  15.324    520
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.42 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.39), residues: 484
  helix:  1.25 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop :  0.05 (0.67), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  29 
 TYR   0.010   0.001   TYR B  21 
 PHE   0.011   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3983)
  covalent geometry    : angle       0.57212 ( 5383)
  hydrogen bonds       : bond        0.03346 (  271)
  hydrogen bonds       : angle       3.93774 (  792)

*********************** 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
  80 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7834 (pt0) cc_final: 0.7598 (pt0)
REVERT: B   42 LYS cc_start: 0.8103 (tppt) cc_final: 0.7893 (mmtm)
REVERT: B  178 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8119 (tt)
REVERT: B  366 ASP cc_start: 0.8093 (m-30) cc_final: 0.7816 (m-30)
REVERT: B  408 MET cc_start: 0.7245 (ttt) cc_final: 0.6889 (ttt)
REVERT: B  427 GLU cc_start: 0.8491 (pp20) cc_final: 0.7981 (pp20)
  outliers start: 18
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4601
  time to fit residues: 34.7984
Evaluate side-chains
  60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  354 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   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  19 ASN
B 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.119076 restraints weight = 7306.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.72
r_work: 0.3564 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3983  Z= 0.132
  Angle     :  0.593   8.012   5383  Z= 0.300
  Chirality :  0.039   0.141    620
  Planarity :  0.003   0.038    694
  Dihedral  :  3.926  14.861    520
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 26.27 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.39), residues: 484
  helix:  1.15 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.21 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 557 
 TYR   0.014   0.001   TYR B  21 
 PHE   0.013   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3983)
  covalent geometry    : angle       0.59256 ( 5383)
  hydrogen bonds       : bond        0.03301 (  271)
  hydrogen bonds       : angle       3.92311 (  792)

*********************** 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
  74 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.7022 (mt) cc_final: 0.6382 (mp)
REVERT: B   23 GLN cc_start: 0.7900 (pt0) cc_final: 0.7607 (pt0)
REVERT: B  178 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8119 (tt)
REVERT: B  208 ARG cc_start: 0.8220 (mmp80) cc_final: 0.7878 (mmp80)
REVERT: B  366 ASP cc_start: 0.8102 (m-30) cc_final: 0.7826 (m-30)
REVERT: B  408 MET cc_start: 0.7147 (ttt) cc_final: 0.6803 (ttt)
REVERT: B  424 SER cc_start: 0.6928 (OUTLIER) cc_final: 0.6543 (t)
REVERT: B  427 GLU cc_start: 0.8522 (pp20) cc_final: 0.8291 (pp20)
  outliers start: 15
  outliers final: 6
  residues processed: 67
  average time/residue: 0.3747
  time to fit residues: 26.1674
Evaluate side-chains
  64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  225 LEU
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  424 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    0.0570
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.147282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.119409 restraints weight = 7418.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.72
r_work: 0.3570 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1917

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= 0.127
  Angle     :  0.605   9.234   5383  Z= 0.301
  Chirality :  0.039   0.156    620
  Planarity :  0.003   0.027    694
  Dihedral  :  3.908  14.494    520
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.42 %
    Favored  : 69.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.39), residues: 484
  helix:  1.14 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.16 (0.70), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 133 
 TYR   0.012   0.001   TYR B  21 
 PHE   0.014   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3983)
  covalent geometry    : angle       0.60472 ( 5383)
  hydrogen bonds       : bond        0.03183 (  271)
  hydrogen bonds       : angle       3.86182 (  792)

*********************** 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: 12
    poor density    : 65
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6917 (mt) cc_final: 0.6253 (mp)
REVERT: B   23 GLN cc_start: 0.7906 (pt0) cc_final: 0.7644 (pt0)
REVERT: B  178 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8121 (tt)
REVERT: B  366 ASP cc_start: 0.8099 (m-30) cc_final: 0.7862 (m-30)
REVERT: B  408 MET cc_start: 0.7149 (ttt) cc_final: 0.6773 (ttt)
REVERT: B  424 SER cc_start: 0.6972 (OUTLIER) cc_final: 0.6600 (t)
REVERT: B  427 GLU cc_start: 0.8528 (pp20) cc_final: 0.8102 (pp20)
  outliers start: 12
  outliers final: 7
  residues processed: 73
  average time/residue: 0.3883
  time to fit residues: 29.5480
Evaluate side-chains
  62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
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  424 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 268 ASN
B 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.119471 restraints weight = 7408.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.73
r_work: 0.3568 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.1988

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= 0.132
  Angle     :  0.618   9.793   5383  Z= 0.313
  Chirality :  0.039   0.162    620
  Planarity :  0.003   0.022    694
  Dihedral  :  3.959  17.311    520
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 28.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.39), residues: 484
  helix:  1.13 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop :  0.07 (0.69), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 208 
 TYR   0.009   0.001   TYR B  21 
 PHE   0.014   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3983)
  covalent geometry    : angle       0.61827 ( 5383)
  hydrogen bonds       : bond        0.03157 (  271)
  hydrogen bonds       : angle       3.90366 (  792)

*********************** 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
  71 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6962 (mt) cc_final: 0.6304 (mp)
REVERT: B   23 GLN cc_start: 0.7880 (pt0) cc_final: 0.7671 (pt0)
REVERT: B  178 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: B  208 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7915 (mpp-170)
REVERT: B  366 ASP cc_start: 0.8130 (m-30) cc_final: 0.7898 (m-30)
REVERT: B  408 MET cc_start: 0.7118 (ttt) cc_final: 0.6713 (ttt)
REVERT: B  424 SER cc_start: 0.6980 (OUTLIER) cc_final: 0.6586 (t)
REVERT: B  427 GLU cc_start: 0.8458 (pp20) cc_final: 0.8233 (pp20)
  outliers start: 13
  outliers final: 4
  residues processed: 67
  average time/residue: 0.4265
  time to fit residues: 29.6816
Evaluate side-chains
  58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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  254 LYS
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  424 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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  71 HIS
B 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.146878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.118587 restraints weight = 7369.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.65
r_work: 0.3555 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3983  Z= 0.152
  Angle     :  0.647   9.689   5383  Z= 0.327
  Chirality :  0.040   0.174    620
  Planarity :  0.003   0.019    694
  Dihedral  :  4.000  17.863    520
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 29.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.39), residues: 484
  helix:  1.07 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop :  0.02 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 208 
 TYR   0.013   0.001   TYR B  21 
 PHE   0.012   0.002   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3983)
  covalent geometry    : angle       0.64685 ( 5383)
  hydrogen bonds       : bond        0.03378 (  271)
  hydrogen bonds       : angle       3.99662 (  792)

*********************** 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
  65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8802 (tp) cc_final: 0.8580 (tp)
REVERT: A  607 LEU cc_start: 0.7211 (mt) cc_final: 0.6541 (mp)
REVERT: B   23 GLN cc_start: 0.7916 (pt0) cc_final: 0.7696 (pt0)
REVERT: B  178 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8170 (tt)
REVERT: B  208 ARG cc_start: 0.8312 (mmp80) cc_final: 0.7887 (mpp-170)
REVERT: B  366 ASP cc_start: 0.8112 (m-30) cc_final: 0.7872 (m-30)
REVERT: B  408 MET cc_start: 0.7120 (ttt) cc_final: 0.6711 (ttt)
REVERT: B  424 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6775 (t)
REVERT: B  427 GLU cc_start: 0.8526 (pp20) cc_final: 0.8297 (pp20)
  outliers start: 11
  outliers final: 7
  residues processed: 61
  average time/residue: 0.3954
  time to fit residues: 25.1612
Evaluate side-chains
  60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
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  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  424 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    0.0270
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.5838

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.148166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.120154 restraints weight = 7447.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.65
r_work: 0.3583 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3983  Z= 0.131
  Angle     :  0.672  11.131   5383  Z= 0.333
  Chirality :  0.039   0.136    620
  Planarity :  0.003   0.019    694
  Dihedral  :  3.960  18.039    520
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 30.65 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.39), residues: 484
  helix:  1.11 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.06 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 208 
 TYR   0.036   0.001   TYR B  21 
 PHE   0.013   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3983)
  covalent geometry    : angle       0.67237 ( 5383)
  hydrogen bonds       : bond        0.03166 (  271)
  hydrogen bonds       : angle       3.94989 (  792)

*********************** 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
  64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8802 (tp) cc_final: 0.8572 (tp)
REVERT: A  607 LEU cc_start: 0.7166 (mt) cc_final: 0.6496 (mp)
REVERT: B   23 GLN cc_start: 0.7892 (pt0) cc_final: 0.7682 (pt0)
REVERT: B  178 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8160 (tt)
REVERT: B  208 ARG cc_start: 0.8303 (mmp80) cc_final: 0.7887 (mpp-170)
REVERT: B  366 ASP cc_start: 0.8139 (m-30) cc_final: 0.7890 (m-30)
REVERT: B  424 SER cc_start: 0.7107 (OUTLIER) cc_final: 0.6731 (t)
REVERT: B  427 GLU cc_start: 0.8520 (pp20) cc_final: 0.8114 (pp20)
  outliers start: 10
  outliers final: 6
  residues processed: 60
  average time/residue: 0.4148
  time to fit residues: 25.9423
Evaluate side-chains
  63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  424 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 47 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.7780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.148071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.119796 restraints weight = 7375.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.69
r_work: 0.3580 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2303

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= 0.143
  Angle     :  0.692  11.265   5383  Z= 0.343
  Chirality :  0.040   0.154    620
  Planarity :  0.003   0.021    694
  Dihedral  :  4.001  18.018    520
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 30.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.39), residues: 484
  helix:  1.03 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop :  0.05 (0.69), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 208 
 TYR   0.011   0.001   TYR B  21 
 PHE   0.013   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3983)
  covalent geometry    : angle       0.69201 ( 5383)
  hydrogen bonds       : bond        0.03238 (  271)
  hydrogen bonds       : angle       4.03917 (  792)

********************** 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
  64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8812 (tp) cc_final: 0.8583 (tp)
REVERT: A  607 LEU cc_start: 0.7207 (mt) cc_final: 0.6523 (mp)
REVERT: B   23 GLN cc_start: 0.7884 (pt0) cc_final: 0.7680 (pt0)
REVERT: B  178 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: B  208 ARG cc_start: 0.8312 (mmp80) cc_final: 0.7948 (mmp80)
REVERT: B  366 ASP cc_start: 0.8166 (m-30) cc_final: 0.7946 (m-30)
REVERT: B  424 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6724 (t)
REVERT: B  427 GLU cc_start: 0.8440 (pp20) cc_final: 0.8212 (pp20)
REVERT: B  440 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6988 (pm20)
  outliers start: 11
  outliers final: 8
  residues processed: 60
  average time/residue: 0.4123
  time to fit residues: 25.8680
Evaluate side-chains
  63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
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  424 SER
Chi-restraints excluded: chain B residue  440 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7560

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.148079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.119819 restraints weight = 7291.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.68
r_work: 0.3584 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2309

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= 0.139
  Angle     :  0.685  11.278   5383  Z= 0.341
  Chirality :  0.040   0.150    620
  Planarity :  0.003   0.022    694
  Dihedral  :  4.001  18.127    520
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 30.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.39), residues: 484
  helix:  1.01 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop :  0.08 (0.70), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 208 
 TYR   0.021   0.001   TYR B  21 
 PHE   0.013   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3983)
  covalent geometry    : angle       0.68501 ( 5383)
  hydrogen bonds       : bond        0.03222 (  271)
  hydrogen bonds       : angle       4.03318 (  792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1322.00 seconds
wall clock time: 23 minutes 18.86 seconds (1398.86 seconds total)