Starting phenix.real_space_refine
on Sun Mar 10 18:23:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_18674.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_18674.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_18674.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_18674.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/03_2024/8qvw_18674.pdb"
  }
  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
    Residue "B GLU  146": "OE1" <-> "OE2"
    Residue "B GLU  374": "OE1" <-> "OE2"
    Residue "B ASP  423": "OD1" <-> "OD2"
    Residue "B PHE  429": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.64, per 1000 atoms: 0.67
  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  - 3.50
        Amino acid           : False - 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: 1.66
  Conformation dependent library (CDL) restraints added in 648.4 milliseconds
  

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

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

    271 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.79 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:
       98.74 -   105.79: 70
      105.79 -   112.84: 2178
      112.84 -   119.89: 1351
      119.89 -   126.94: 1746
      126.94 -   133.99: 38
  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 2.440
  nonbonded pdb=" N   GLU B 146 "
            pdb=" OE1 GLU B 146 "
     model   vdw
     2.247 2.520
  nonbonded pdb=" O   ASN B 278 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.275 2.440
  nonbonded pdb=" OD1 ASP B 141 "
            pdb=" NH1 ARG B 147 "
     model   vdw
     2.286 2.520
  nonbonded pdb=" O   LEU B 313 "
            pdb=" OG1 THR B 317 "
     model   vdw
     2.299 2.440
  ... (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
========== 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:             0.240
  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:          1.460
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.020
  Find NCS groups from input model:        0.100
  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:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.560
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.456 
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: 0.9661
  time to fit residues: 65.5142
Evaluate side-chains
  59 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1091

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= 0.185
  Angle     :  0.553   7.466   5383  Z= 0.284
  Chirality :  0.038   0.135    620
  Planarity :  0.003   0.028    694
  Dihedral  :  3.956  16.814    520
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.50 %
    Favored  : 70.74 %
  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:  1.51 (0.39), residues: 484
  helix:  1.32 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.10 (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   0.011   0.001   PHE B 429 
 TYR   0.013   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
  74 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  137 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6817 (ttp-170)
REVERT: B  366 ASP cc_start: 0.7758 (m-30) cc_final: 0.7541 (m-30)
REVERT: B  408 MET cc_start: 0.7415 (ttt) cc_final: 0.7101 (ttt)
REVERT: B  427 GLU cc_start: 0.8314 (pp20) cc_final: 0.7941 (pp20)
  outliers start: 12
  outliers final: 4
  residues processed: 68
  average time/residue: 0.9816
  time to fit residues: 69.7683
Evaluate side-chains
  62 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  329 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 353 GLN
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1315

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= 0.189
  Angle     :  0.563   8.274   5383  Z= 0.284
  Chirality :  0.038   0.134    620
  Planarity :  0.003   0.019    694
  Dihedral  :  3.924  16.161    520
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.42 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.39), residues: 484
  helix:  1.30 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.03 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.008   0.001   TYR B  86 
 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
  78 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A  570 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8146 (mmmt)
REVERT: B   23 GLN cc_start: 0.7852 (pt0) cc_final: 0.7632 (pt0)
REVERT: B   29 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7278 (mpp80)
REVERT: B  366 ASP cc_start: 0.7771 (m-30) cc_final: 0.7540 (m-30)
REVERT: B  408 MET cc_start: 0.7414 (ttt) cc_final: 0.7065 (ttt)
  outliers start: 16
  outliers final: 6
  residues processed: 72
  average time/residue: 1.0249
  time to fit residues: 76.8481
Evaluate side-chains
  64 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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   98 LEU
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  354 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 GLN
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1475

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= 0.196
  Angle     :  0.558   7.581   5383  Z= 0.283
  Chirality :  0.038   0.141    620
  Planarity :  0.003   0.022    694
  Dihedral  :  3.890  15.715    520
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 26.73 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.39), residues: 484
  helix:  1.30 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.04 (0.66), residues: 108

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   0.009   0.001   TYR B  86 
 ARG   0.002   0.000   ARG B  29 

*********************** 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
  82 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6861 (mt) cc_final: 0.6505 (mt)
REVERT: B   21 TYR cc_start: 0.5442 (t80) cc_final: 0.3904 (t80)
REVERT: B   23 GLN cc_start: 0.7874 (pt0) cc_final: 0.7662 (pt0)
REVERT: B  126 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6988 (m-30)
REVERT: B  178 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8188 (tt)
REVERT: B  366 ASP cc_start: 0.7798 (m-30) cc_final: 0.7542 (m-30)
REVERT: B  408 MET cc_start: 0.7293 (ttt) cc_final: 0.6966 (ttt)
  outliers start: 19
  outliers final: 6
  residues processed: 74
  average time/residue: 1.0122
  time to fit residues: 78.0408
Evaluate side-chains
  64 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
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  126 ASP
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  329 SER
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 34 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 331 GLN
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3983  Z= 0.277
  Angle     :  0.617   8.718   5383  Z= 0.310
  Chirality :  0.041   0.156    620
  Planarity :  0.003   0.028    694
  Dihedral  :  3.989  16.439    520
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.96 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.39), residues: 484
  helix:  0.98 (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   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B  71 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.012   0.002   TYR B  86 
 ARG   0.007   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
  81 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6936 (mt) cc_final: 0.6480 (mt)
REVERT: B   23 GLN cc_start: 0.8019 (pt0) cc_final: 0.7740 (pt0)
REVERT: B  126 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7025 (m-30)
REVERT: B  178 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8326 (tt)
  outliers start: 18
  outliers final: 10
  residues processed: 75
  average time/residue: 0.9143
  time to fit residues: 71.6533
Evaluate side-chains
  71 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  126 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  289 THR
Chi-restraints excluded: chain B residue  329 SER
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  410 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 GLN
B 331 GLN
B 347 GLN
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1950

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= 0.250
  Angle     :  0.600   8.690   5383  Z= 0.303
  Chirality :  0.040   0.136    620
  Planarity :  0.003   0.035    694
  Dihedral  :  3.998  16.214    520
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.88 %
    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:  0.93 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.02 (0.68), residues: 101

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   0.015   0.001   PHE B 429 
 TYR   0.012   0.002   TYR B  86 
 ARG   0.010   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
  82 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6994 (mt) cc_final: 0.6556 (mt)
REVERT: B   23 GLN cc_start: 0.8024 (pt0) cc_final: 0.7790 (pt0)
REVERT: B  126 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7033 (m-30)
REVERT: B  178 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: B  382 LEU cc_start: 0.8250 (mm) cc_final: 0.7981 (mm)
  outliers start: 20
  outliers final: 11
  residues processed: 76
  average time/residue: 0.8816
  time to fit residues: 70.1276
Evaluate side-chains
  66 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  126 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  289 THR
Chi-restraints excluded: chain B residue  329 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0000
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 GLN
B 347 GLN
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3983  Z= 0.173
  Angle     :  0.595  10.083   5383  Z= 0.297
  Chirality :  0.038   0.135    620
  Planarity :  0.003   0.033    694
  Dihedral  :  3.917  15.147    520
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 29.26 %
    Favored  : 66.13 %
  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 (0.39), residues: 484
  helix:  1.11 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.10 (0.68), residues: 103

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   0.014   0.001   PHE B 429 
 TYR   0.008   0.001   TYR B 132 
 ARG   0.008   0.001   ARG B 133 

*********************** 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
  82 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8713 (tp) cc_final: 0.8463 (tp)
REVERT: A  607 LEU cc_start: 0.6869 (mt) cc_final: 0.6394 (mp)
REVERT: B   23 GLN cc_start: 0.7860 (pt0) cc_final: 0.7602 (pt0)
REVERT: B  126 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6967 (m-30)
REVERT: B  196 MET cc_start: 0.7911 (mmm) cc_final: 0.7628 (tpt)
REVERT: B  382 LEU cc_start: 0.8233 (mm) cc_final: 0.7961 (mm)
  outliers start: 20
  outliers final: 10
  residues processed: 76
  average time/residue: 0.8646
  time to fit residues: 68.8682
Evaluate side-chains
  67 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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  126 ASP
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  410 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0170
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3983  Z= 0.190
  Angle     :  0.623  10.177   5383  Z= 0.307
  Chirality :  0.038   0.134    620
  Planarity :  0.003   0.033    694
  Dihedral  :  3.903  14.776    520
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 30.88 %
    Favored  : 65.90 %
  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:  1.41 (0.39), residues: 484
  helix:  1.28 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.04 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.008   0.001   TYR B  86 
 ARG   0.007   0.001   ARG B 133 

*********************** 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
  73 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8738 (tp) cc_final: 0.8488 (tp)
REVERT: A  607 LEU cc_start: 0.6808 (mt) cc_final: 0.6356 (mt)
REVERT: B  126 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6957 (m-30)
REVERT: B  132 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7019 (t80)
REVERT: B  196 MET cc_start: 0.7937 (mmm) cc_final: 0.7676 (tpt)
REVERT: B  382 LEU cc_start: 0.8198 (mm) cc_final: 0.7913 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 68
  average time/residue: 0.8453
  time to fit residues: 60.4547
Evaluate side-chains
  62 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  132 TYR
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   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  24 ASN
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3983  Z= 0.199
  Angle     :  0.642  10.244   5383  Z= 0.319
  Chirality :  0.038   0.138    620
  Planarity :  0.003   0.027    694
  Dihedral  :  3.937  14.663    520
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 30.65 %
    Favored  : 65.67 %
  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:  1.33 (0.39), residues: 484
  helix:  1.21 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.04 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.009   0.001   TYR B  86 
 ARG   0.007   0.001   ARG B 137 

*********************** 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
  73 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LEU cc_start: 0.6948 (mt) cc_final: 0.6502 (mt)
REVERT: B  126 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6969 (m-30)
REVERT: B  382 LEU cc_start: 0.8260 (mm) cc_final: 0.7968 (mm)
REVERT: B  408 MET cc_start: 0.7310 (ttt) cc_final: 0.7036 (ptm)
  outliers start: 16
  outliers final: 8
  residues processed: 69
  average time/residue: 0.7476
  time to fit residues: 54.3834
Evaluate side-chains
  63 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  410 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3983  Z= 0.211
  Angle     :  0.680  10.538   5383  Z= 0.333
  Chirality :  0.040   0.150    620
  Planarity :  0.003   0.030    694
  Dihedral  :  4.023  14.675    520
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 31.80 %
    Favored  : 65.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.39), residues: 484
  helix:  1.08 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.09 (0.66), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.021   0.002   PHE A 561 
 TYR   0.011   0.001   TYR B  21 
 ARG   0.007   0.001   ARG B 208 

********************** 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
  69 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 LEU cc_start: 0.8680 (tp) cc_final: 0.8430 (tp)
REVERT: A  607 LEU cc_start: 0.6939 (mt) cc_final: 0.6495 (mp)
REVERT: B  126 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6941 (m-30)
REVERT: B  382 LEU cc_start: 0.8265 (mm) cc_final: 0.7969 (mm)
REVERT: B  408 MET cc_start: 0.7353 (ttt) cc_final: 0.7066 (ptm)
  outliers start: 12
  outliers final: 8
  residues processed: 66
  average time/residue: 0.7679
  time to fit residues: 53.4098
Evaluate side-chains
  64 residues out of total 434 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  251 GLN
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  329 SER
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 38 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 455 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 = 0.4093 r_free = 0.4093 target = 0.147428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.119144 restraints weight = 7383.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.70
r_work: 0.3567 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3983  Z= 0.208
  Angle     :  0.678  10.451   5383  Z= 0.333
  Chirality :  0.039   0.137    620
  Planarity :  0.003   0.038    694
  Dihedral  :  4.027  14.613    520
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 32.03 %
    Favored  : 65.21 %
  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:  1.13 (0.39), residues: 484
  helix:  1.05 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.10 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.018   0.001   PHE A 561 
 TYR   0.011   0.001   TYR B  86 
 ARG   0.006   0.001   ARG B 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.56 seconds
wall clock time: 31 minutes 10.29 seconds (1870.29 seconds total)