Starting phenix.real_space_refine
on Mon Jun 24 21:08:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/06_2024/8xw1_38727.pdb"
  }
  resolution = 4.49
  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=   0.006 sd=   0.041
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      24      5.16       5
     C    3378      2.51       5
     N     826      2.21       5
     O     854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   78": "OE1" <-> "OE2"
    Residue "A GLU  195": "OE1" <-> "OE2"
    Residue "A GLU  219": "OE1" <-> "OE2"
    Residue "A GLU  222": "OE1" <-> "OE2"
    Residue "A GLU  292": "OE1" <-> "OE2"
    Residue "A GLU  304": "OE1" <-> "OE2"
    Residue "A GLU  308": "OE1" <-> "OE2"
    Residue "A GLU  461": "OE1" <-> "OE2"
    Residue "A GLU  531": "OE1" <-> "OE2"
    Residue "A GLU  556": "OE1" <-> "OE2"
    Residue "A GLU  616": "OE1" <-> "OE2"
    Residue "A GLU  687": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib"
  Total number of atoms: 5082
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5082
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Time building chain proxies: 3.63, per 1000 atoms: 0.71
  Number of scatterers: 5082
  At special positions: 0
  Unit cell: (92.13, 87.15, 99.6, 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      24     16.00
     O     854      8.00
     N     826      7.00
     C    3378      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: 2.31
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 1 sheets defined
      77.1% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.599A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 3.504A  pdb=" N   TYR A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.835A  pdb=" N   GLU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 92 through 119
      removed outlier: 4.175A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 194
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 6.155A  pdb=" N   LYS A 317 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 319 " --> pdb=" O   PRO A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 355 through 359
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.559A  pdb=" N   ALA A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.708A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 3.952A  pdb=" N   GLN A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 430  - end of helix
      removed outlier: 4.544A  pdb=" N   PHE A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 476
    Processing helix  chain 'A' and resid 477 through 490
      removed outlier: 4.486A  pdb=" N   LEU A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 512 through 524
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 553 through 559
      removed outlier: 4.381A  pdb=" N   GLU A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 589 through 612
      removed outlier: 4.316A  pdb=" N   PHE A 593 " --> pdb=" O   MET A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 654 through 659
      removed outlier: 3.717A  pdb=" N   LEU A 658 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 4.095A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 3.539A  pdb=" N   TYR A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 238
      removed outlier: 3.902A  pdb=" N   THR A 235 " --> pdb=" O   SER A 326 " (cutoff:3.500A)

    341 hydrogen bonds defined for protein.
    999 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: 1.93

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1541
        1.34 -     1.46: 994
        1.46 -     1.57: 2649
        1.57 -     1.69: 1
        1.69 -     1.81: 44
  Bond restraints: 5229
  Sorted by residual:
  bond pdb=" CG  PRO A  77 "
       pdb=" CD  PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.503  1.421  0.082 3.40e-02 8.65e+02 5.81e+00
  bond pdb=" CB  PRO A  77 "
       pdb=" CG  PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.492  1.590 -0.098 5.00e-02 4.00e+02 3.83e+00
  bond pdb=" N   TRP A 335 "
       pdb=" CA  TRP A 335 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.19e-02 7.06e+03 3.79e+00
  bond pdb=" CG  LEU A 120 "
       pdb=" CD2 LEU A 120 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.94e+00
  bond pdb=" C   TRP A 335 "
       pdb=" O   TRP A 335 "
    ideal  model  delta    sigma   weight residual
    1.236  1.221  0.015 1.15e-02 7.56e+03 1.74e+00
  ... (remaining 5224 not shown)

  Histogram of bond angle deviations from ideal:
       96.34 -   103.90: 96
      103.90 -   111.46: 2321
      111.46 -   119.02: 1857
      119.02 -   126.57: 2740
      126.57 -   134.13: 99
  Bond angle restraints: 7113
  Sorted by residual:
  angle pdb=" N   LYS A 503 "
        pdb=" CA  LYS A 503 "
        pdb=" C   LYS A 503 "
      ideal   model   delta    sigma   weight residual
     112.88  106.35    6.53 1.29e+00 6.01e-01 2.56e+01
  angle pdb=" N   PRO A  77 "
        pdb=" CD  PRO A  77 "
        pdb=" CG  PRO A  77 "
      ideal   model   delta    sigma   weight residual
     103.20   96.34    6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" CA  PRO A  77 "
        pdb=" N   PRO A  77 "
        pdb=" CD  PRO A  77 "
      ideal   model   delta    sigma   weight residual
     112.00  105.67    6.33 1.40e+00 5.10e-01 2.04e+01
  angle pdb=" C   PHE A 109 "
        pdb=" N   THR A 110 "
        pdb=" CA  THR A 110 "
      ideal   model   delta    sigma   weight residual
     119.83  116.17    3.66 1.11e+00 8.12e-01 1.09e+01
  angle pdb=" C   ASP A 552 "
        pdb=" N   LYS A 553 "
        pdb=" CA  LYS A 553 "
      ideal   model   delta    sigma   weight residual
     121.54  127.51   -5.97 1.91e+00 2.74e-01 9.78e+00
  ... (remaining 7108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 2764
       16.55 -    33.10: 239
       33.10 -    49.65: 42
       49.65 -    66.21: 9
       66.21 -    82.76: 11
  Dihedral angle restraints: 3065
    sinusoidal: 1194
      harmonic: 1871
  Sorted by residual:
  dihedral pdb=" CA  PHE A 440 "
           pdb=" C   PHE A 440 "
           pdb=" N   LEU A 441 "
           pdb=" CA  LEU A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.21  -19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLN A 340 "
           pdb=" C   GLN A 340 "
           pdb=" N   GLN A 341 "
           pdb=" CA  GLN A 341 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.68  -19.32     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  MET A  82 "
           pdb=" C   MET A  82 "
           pdb=" N   PRO A  83 "
           pdb=" CA  PRO A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 3062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 587
       0.045 -    0.091: 165
       0.091 -    0.136: 43
       0.136 -    0.181: 4
       0.181 -    0.226: 2
  Chirality restraints: 801
  Sorted by residual:
  chirality pdb=" CB  VAL A 119 "
            pdb=" CA  VAL A 119 "
            pdb=" CG1 VAL A 119 "
            pdb=" CG2 VAL A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  LYS A 536 "
            pdb=" N   LYS A 536 "
            pdb=" C   LYS A 536 "
            pdb=" CB  LYS A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CA  GLU A 311 "
            pdb=" N   GLU A 311 "
            pdb=" C   GLU A 311 "
            pdb=" CB  GLU A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  ... (remaining 798 not shown)

  Planarity restraints: 882
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  76 "    0.047 5.00e-02 4.00e+02   6.81e-02 7.43e+00
        pdb=" N   PRO A  77 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 307 "    0.014 2.00e-02 2.50e+03   2.70e-02 7.30e+00
        pdb=" C   LYS A 307 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS A 307 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU A 308 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 352 "    0.015 2.00e-02 2.50e+03   1.12e-02 3.13e+00
        pdb=" CG  TRP A 352 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 352 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 352 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 352 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 352 "    0.006 2.00e-02 2.50e+03
  ... (remaining 879 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 144
        2.69 -     3.24: 5891
        3.24 -     3.80: 8715
        3.80 -     4.35: 10301
        4.35 -     4.90: 16226
  Nonbonded interactions: 41277
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.139 2.440
  nonbonded pdb=" OE1 GLU A  78 "
            pdb=" NZ  LYS A  81 "
     model   vdw
     2.178 2.520
  nonbonded pdb=" O   PHE A 224 "
            pdb=" ND2 ASN A 228 "
     model   vdw
     2.215 2.520
  nonbonded pdb=" O   TRP A 335 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.221 2.440
  nonbonded pdb=" O   LEU A 635 "
            pdb=" OG  SER A 638 "
     model   vdw
     2.234 2.440
  ... (remaining 41272 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.940
  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:          3.460
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.590
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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      :  0.005   0.098   5229  Z= 0.332
  Angle     :  0.821   7.921   7113  Z= 0.465
  Chirality :  0.046   0.226    801
  Planarity :  0.005   0.068    882
  Dihedral  : 14.015  82.757   1849
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.95 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.33), residues: 624
  helix:  0.75 (0.25), residues: 417
  sheet: -2.19 (1.07), residues: 16
  loop : -1.55 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 352 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.023   0.002   PHE A 437 
 TYR   0.024   0.002   TYR A 469 
 ARG   0.013   0.001   ARG A 462 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 TYR cc_start: 0.8095 (m-80) cc_final: 0.6785 (m-80)
REVERT: A   82 MET cc_start: 0.9014 (tpt) cc_final: 0.8787 (tpp)
REVERT: A  109 PHE cc_start: 0.9600 (m-10) cc_final: 0.9385 (m-10)
REVERT: A  178 MET cc_start: 0.9286 (ppp) cc_final: 0.9031 (ppp)
REVERT: A  180 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9069 (tp30)
REVERT: A  262 TYR cc_start: 0.9429 (m-80) cc_final: 0.8995 (m-80)
REVERT: A  305 ILE cc_start: 0.9548 (pt) cc_final: 0.9301 (pt)
REVERT: A  355 GLU cc_start: 0.9432 (tp30) cc_final: 0.9123 (tp30)
REVERT: A  437 PHE cc_start: 0.8999 (m-80) cc_final: 0.8594 (m-80)
REVERT: A  440 PHE cc_start: 0.8716 (m-10) cc_final: 0.8451 (t80)
REVERT: A  461 GLU cc_start: 0.9164 (tp30) cc_final: 0.8754 (mm-30)
REVERT: A  475 ASN cc_start: 0.9007 (m110) cc_final: 0.8642 (m110)
REVERT: A  511 MET cc_start: 0.9194 (mmp) cc_final: 0.8965 (mmm)
REVERT: A  532 ILE cc_start: 0.9414 (tt) cc_final: 0.9171 (tt)
REVERT: A  677 GLU cc_start: 0.8620 (pt0) cc_final: 0.8376 (pt0)
REVERT: A  710 ASN cc_start: 0.9388 (m-40) cc_final: 0.9166 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1438
  time to fit residues: 34.1677
Evaluate side-chains
  136 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 229 HIS
A 363 ASN
A 397 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5229  Z= 0.199
  Angle     :  0.645   7.774   7113  Z= 0.325
  Chirality :  0.043   0.283    801
  Planarity :  0.004   0.038    882
  Dihedral  :  4.699  18.181    680
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.16 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.35), residues: 624
  helix:  1.51 (0.25), residues: 422
  sheet: -2.02 (1.10), residues: 16
  loop : -1.42 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.027   0.002   PHE A 437 
 TYR   0.014   0.001   TYR A  98 
 ARG   0.007   0.001   ARG A 309 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9336 (m-30) cc_final: 0.9025 (m-30)
REVERT: A   38 TYR cc_start: 0.8215 (m-80) cc_final: 0.6917 (m-80)
REVERT: A   82 MET cc_start: 0.9115 (tpt) cc_final: 0.8902 (tpt)
REVERT: A  165 MET cc_start: 0.9441 (mmp) cc_final: 0.9227 (mmp)
REVERT: A  178 MET cc_start: 0.9225 (ppp) cc_final: 0.8996 (ppp)
REVERT: A  180 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9125 (tp30)
REVERT: A  262 TYR cc_start: 0.9457 (m-80) cc_final: 0.9067 (m-80)
REVERT: A  309 ARG cc_start: 0.8873 (mmp80) cc_final: 0.8547 (mmp80)
REVERT: A  320 MET cc_start: 0.8543 (mmp) cc_final: 0.8163 (mmm)
REVERT: A  368 TYR cc_start: 0.8778 (t80) cc_final: 0.8266 (t80)
REVERT: A  437 PHE cc_start: 0.8979 (m-80) cc_final: 0.8585 (m-80)
REVERT: A  445 LEU cc_start: 0.9785 (mt) cc_final: 0.9580 (mt)
REVERT: A  461 GLU cc_start: 0.9222 (tp30) cc_final: 0.8748 (mm-30)
REVERT: A  476 VAL cc_start: 0.9318 (t) cc_final: 0.9118 (t)
REVERT: A  511 MET cc_start: 0.9168 (mmp) cc_final: 0.8929 (mmm)
REVERT: A  532 ILE cc_start: 0.9438 (tt) cc_final: 0.9100 (tt)
REVERT: A  540 MET cc_start: 0.9620 (mmp) cc_final: 0.9291 (mmp)
REVERT: A  613 TYR cc_start: 0.9209 (m-80) cc_final: 0.8935 (m-80)
REVERT: A  624 TRP cc_start: 0.9052 (t-100) cc_final: 0.8761 (t-100)
REVERT: A  661 LEU cc_start: 0.9763 (mt) cc_final: 0.9159 (mt)
REVERT: A  689 MET cc_start: 0.9456 (mmp) cc_final: 0.9256 (mmm)
REVERT: A  690 MET cc_start: 0.9337 (mmt) cc_final: 0.8980 (tpt)
REVERT: A  710 ASN cc_start: 0.9327 (m-40) cc_final: 0.9121 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 0.1342
  time to fit residues: 32.3032
Evaluate side-chains
  144 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    0.0870
   chunk 17 optimal weight:    0.4980
   chunk 47 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.3164

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5229  Z= 0.262
  Angle     :  0.656  10.709   7113  Z= 0.334
  Chirality :  0.041   0.174    801
  Planarity :  0.004   0.034    882
  Dihedral  :  4.593  17.132    680
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.09 (0.36), residues: 624
  helix:  1.69 (0.26), residues: 422
  sheet: -2.03 (1.39), residues: 11
  loop : -1.34 (0.50), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 352 
 HIS   0.006   0.001   HIS A 628 
 PHE   0.022   0.002   PHE A 428 
 TYR   0.011   0.001   TYR A  98 
 ARG   0.004   0.000   ARG A 309 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9363 (m-30) cc_final: 0.9027 (m-30)
REVERT: A   38 TYR cc_start: 0.8277 (m-80) cc_final: 0.6983 (m-80)
REVERT: A  262 TYR cc_start: 0.9492 (m-80) cc_final: 0.9282 (m-80)
REVERT: A  320 MET cc_start: 0.8682 (mmp) cc_final: 0.8261 (mmm)
REVERT: A  355 GLU cc_start: 0.9404 (tp30) cc_final: 0.9172 (tp30)
REVERT: A  368 TYR cc_start: 0.8595 (t80) cc_final: 0.8382 (t80)
REVERT: A  437 PHE cc_start: 0.9075 (m-80) cc_final: 0.8633 (m-80)
REVERT: A  445 LEU cc_start: 0.9791 (mt) cc_final: 0.9588 (mt)
REVERT: A  475 ASN cc_start: 0.9072 (m110) cc_final: 0.8547 (m110)
REVERT: A  511 MET cc_start: 0.9221 (mmp) cc_final: 0.8959 (mmm)
REVERT: A  532 ILE cc_start: 0.9457 (tt) cc_final: 0.9091 (tt)
REVERT: A  540 MET cc_start: 0.9617 (mmp) cc_final: 0.9290 (mmp)
REVERT: A  579 LEU cc_start: 0.9704 (mt) cc_final: 0.9419 (mt)
REVERT: A  604 VAL cc_start: 0.9804 (t) cc_final: 0.9549 (t)
REVERT: A  613 TYR cc_start: 0.9305 (m-80) cc_final: 0.8928 (m-80)
REVERT: A  677 GLU cc_start: 0.8568 (pt0) cc_final: 0.8360 (pt0)
REVERT: A  682 ARG cc_start: 0.8563 (mpt-90) cc_final: 0.8103 (ttm110)
REVERT: A  689 MET cc_start: 0.9454 (mmp) cc_final: 0.9253 (mmm)
REVERT: A  690 MET cc_start: 0.9344 (mmt) cc_final: 0.8981 (tpt)
REVERT: A  710 ASN cc_start: 0.9336 (m-40) cc_final: 0.9126 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1348
  time to fit residues: 31.4034
Evaluate side-chains
  132 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:    0.0060
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0030
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7610

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5229  Z= 0.176
  Angle     :  0.607   7.336   7113  Z= 0.308
  Chirality :  0.041   0.179    801
  Planarity :  0.004   0.036    882
  Dihedral  :  4.403  17.297    680
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.19 (0.36), residues: 624
  helix:  1.78 (0.26), residues: 422
  sheet: -1.78 (1.45), residues: 11
  loop : -1.35 (0.49), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 293 
 PHE   0.019   0.002   PHE A 428 
 TYR   0.009   0.001   TYR A  98 
 ARG   0.003   0.000   ARG A 630 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9354 (m-30) cc_final: 0.8967 (m-30)
REVERT: A   38 TYR cc_start: 0.8173 (m-80) cc_final: 0.6782 (m-80)
REVERT: A   76 MET cc_start: 0.9594 (mmm) cc_final: 0.9251 (mmm)
REVERT: A   82 MET cc_start: 0.9128 (tpt) cc_final: 0.8880 (tpt)
REVERT: A  157 MET cc_start: 0.7886 (pmm) cc_final: 0.7580 (ptm)
REVERT: A  165 MET cc_start: 0.9406 (mmp) cc_final: 0.9118 (mmp)
REVERT: A  180 GLU cc_start: 0.9243 (tm-30) cc_final: 0.9042 (tp30)
REVERT: A  304 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9182 (pt0)
REVERT: A  319 ILE cc_start: 0.9305 (mp) cc_final: 0.8877 (mp)
REVERT: A  320 MET cc_start: 0.8653 (mmp) cc_final: 0.8175 (mmm)
REVERT: A  355 GLU cc_start: 0.9355 (tp30) cc_final: 0.9153 (tp30)
REVERT: A  396 VAL cc_start: 0.9623 (t) cc_final: 0.9403 (t)
REVERT: A  399 LEU cc_start: 0.9718 (mt) cc_final: 0.9483 (mt)
REVERT: A  437 PHE cc_start: 0.9075 (m-80) cc_final: 0.8433 (m-80)
REVERT: A  469 TYR cc_start: 0.9536 (t80) cc_final: 0.9323 (t80)
REVERT: A  511 MET cc_start: 0.9198 (mmp) cc_final: 0.8935 (mmm)
REVERT: A  534 MET cc_start: 0.9415 (mpp) cc_final: 0.9143 (mpp)
REVERT: A  540 MET cc_start: 0.9611 (mmp) cc_final: 0.9288 (mmp)
REVERT: A  682 ARG cc_start: 0.8531 (mpt-90) cc_final: 0.8028 (ttm110)
REVERT: A  690 MET cc_start: 0.9311 (mmt) cc_final: 0.8940 (tpt)
REVERT: A  710 ASN cc_start: 0.9295 (m-40) cc_final: 0.9079 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1284
  time to fit residues: 30.0605
Evaluate side-chains
  131 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0980
   chunk 15 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5229  Z= 0.170
  Angle     :  0.592   7.876   7113  Z= 0.299
  Chirality :  0.040   0.176    801
  Planarity :  0.004   0.037    882
  Dihedral  :  4.283  19.284    680
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.19 (0.36), residues: 624
  helix:  1.71 (0.26), residues: 430
  sheet: -1.66 (1.44), residues: 11
  loop : -1.30 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 162 
 PHE   0.018   0.001   PHE A 428 
 TYR   0.011   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A 630 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9350 (m-30) cc_final: 0.8934 (m-30)
REVERT: A   38 TYR cc_start: 0.8184 (m-80) cc_final: 0.6728 (m-80)
REVERT: A   76 MET cc_start: 0.9540 (mmm) cc_final: 0.9184 (mmm)
REVERT: A   82 MET cc_start: 0.9120 (tpt) cc_final: 0.8834 (tpt)
REVERT: A  157 MET cc_start: 0.7846 (pmm) cc_final: 0.7588 (ptm)
REVERT: A  180 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8887 (tm-30)
REVERT: A  262 TYR cc_start: 0.9430 (m-80) cc_final: 0.9165 (m-80)
REVERT: A  355 GLU cc_start: 0.9355 (tp30) cc_final: 0.9144 (tp30)
REVERT: A  396 VAL cc_start: 0.9616 (t) cc_final: 0.9351 (t)
REVERT: A  399 LEU cc_start: 0.9726 (mt) cc_final: 0.9499 (mt)
REVERT: A  437 PHE cc_start: 0.9095 (m-80) cc_final: 0.8283 (m-80)
REVERT: A  469 TYR cc_start: 0.9565 (t80) cc_final: 0.9284 (t80)
REVERT: A  511 MET cc_start: 0.9148 (mmp) cc_final: 0.8901 (mmm)
REVERT: A  532 ILE cc_start: 0.9615 (tt) cc_final: 0.9108 (tt)
REVERT: A  533 LEU cc_start: 0.9409 (mm) cc_final: 0.8747 (mm)
REVERT: A  534 MET cc_start: 0.9448 (mpp) cc_final: 0.9063 (mpp)
REVERT: A  540 MET cc_start: 0.9601 (mmp) cc_final: 0.9289 (mmp)
REVERT: A  677 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8896 (pt0)
REVERT: A  682 ARG cc_start: 0.8553 (mpt-90) cc_final: 0.8110 (ttm110)
REVERT: A  710 ASN cc_start: 0.9267 (m-40) cc_final: 0.9027 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1292
  time to fit residues: 30.4571
Evaluate side-chains
  132 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5229  Z= 0.164
  Angle     :  0.589   7.610   7113  Z= 0.296
  Chirality :  0.041   0.179    801
  Planarity :  0.004   0.039    882
  Dihedral  :  4.192  19.428    680
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.08 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.39 (0.36), residues: 624
  helix:  1.86 (0.26), residues: 424
  sheet: -1.76 (1.41), residues: 11
  loop : -1.11 (0.50), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 162 
 PHE   0.017   0.002   PHE A  19 
 TYR   0.010   0.001   TYR A 167 
 ARG   0.001   0.000   ARG A 630 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9332 (m-30) cc_final: 0.8889 (m-30)
REVERT: A   38 TYR cc_start: 0.8152 (m-80) cc_final: 0.6560 (m-80)
REVERT: A   82 MET cc_start: 0.9121 (tpt) cc_final: 0.8848 (tpt)
REVERT: A  157 MET cc_start: 0.7796 (pmm) cc_final: 0.7398 (ptm)
REVERT: A  180 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8842 (tm-30)
REVERT: A  262 TYR cc_start: 0.9447 (m-80) cc_final: 0.9122 (m-80)
REVERT: A  320 MET cc_start: 0.8726 (tpp) cc_final: 0.8248 (ttt)
REVERT: A  355 GLU cc_start: 0.9330 (tp30) cc_final: 0.9130 (tp30)
REVERT: A  437 PHE cc_start: 0.9114 (m-80) cc_final: 0.8259 (m-80)
REVERT: A  445 LEU cc_start: 0.9779 (mt) cc_final: 0.9565 (mt)
REVERT: A  469 TYR cc_start: 0.9613 (t80) cc_final: 0.9217 (t80)
REVERT: A  476 VAL cc_start: 0.9236 (t) cc_final: 0.9015 (t)
REVERT: A  511 MET cc_start: 0.9176 (mmp) cc_final: 0.8917 (mmm)
REVERT: A  532 ILE cc_start: 0.9642 (tt) cc_final: 0.9046 (tt)
REVERT: A  534 MET cc_start: 0.9473 (mpp) cc_final: 0.9015 (mpp)
REVERT: A  540 MET cc_start: 0.9594 (mmp) cc_final: 0.9303 (mmp)
REVERT: A  626 ASP cc_start: 0.8889 (m-30) cc_final: 0.8616 (m-30)
REVERT: A  682 ARG cc_start: 0.8604 (mpt-90) cc_final: 0.8046 (ttm110)
REVERT: A  710 ASN cc_start: 0.9230 (m-40) cc_final: 0.8981 (m-40)
  outliers start: 1
  outliers final: 1
  residues processed: 172
  average time/residue: 0.1214
  time to fit residues: 28.6339
Evaluate side-chains
  130 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0050
   chunk 51 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5229  Z= 0.178
  Angle     :  0.618   8.014   7113  Z= 0.311
  Chirality :  0.040   0.177    801
  Planarity :  0.004   0.036    882
  Dihedral  :  4.224  19.731    680
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.36), residues: 624
  helix:  1.83 (0.26), residues: 425
  sheet: -1.82 (1.41), residues: 11
  loop : -1.13 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  75 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.026   0.001   PHE A 454 
 TYR   0.009   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A 630 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9323 (m-30) cc_final: 0.8860 (m-30)
REVERT: A   38 TYR cc_start: 0.8158 (m-80) cc_final: 0.6509 (m-80)
REVERT: A   76 MET cc_start: 0.9541 (mmm) cc_final: 0.9261 (mmm)
REVERT: A  157 MET cc_start: 0.7823 (pmm) cc_final: 0.7546 (ptm)
REVERT: A  180 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8864 (tm-30)
REVERT: A  262 TYR cc_start: 0.9472 (m-80) cc_final: 0.8924 (m-80)
REVERT: A  320 MET cc_start: 0.8689 (tpp) cc_final: 0.8199 (ttt)
REVERT: A  437 PHE cc_start: 0.9141 (m-80) cc_final: 0.8313 (m-80)
REVERT: A  469 TYR cc_start: 0.9623 (t80) cc_final: 0.9233 (t80)
REVERT: A  476 VAL cc_start: 0.9292 (t) cc_final: 0.9072 (t)
REVERT: A  511 MET cc_start: 0.9144 (mmp) cc_final: 0.8895 (mmm)
REVERT: A  532 ILE cc_start: 0.9626 (tt) cc_final: 0.9036 (tt)
REVERT: A  534 MET cc_start: 0.9486 (mpp) cc_final: 0.8988 (mpp)
REVERT: A  540 MET cc_start: 0.9609 (mmp) cc_final: 0.9305 (mmp)
REVERT: A  668 PHE cc_start: 0.9020 (t80) cc_final: 0.8806 (t80)
REVERT: A  672 CYS cc_start: 0.9265 (p) cc_final: 0.9005 (p)
REVERT: A  682 ARG cc_start: 0.8591 (mpt-90) cc_final: 0.8055 (ttm110)
REVERT: A  710 ASN cc_start: 0.9233 (m-40) cc_final: 0.8997 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1290
  time to fit residues: 30.2725
Evaluate side-chains
  136 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5229  Z= 0.169
  Angle     :  0.624   7.754   7113  Z= 0.315
  Chirality :  0.041   0.192    801
  Planarity :  0.004   0.041    882
  Dihedral  :  4.182  19.112    680
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.28 (0.35), residues: 624
  helix:  1.76 (0.26), residues: 426
  sheet: -1.70 (1.41), residues: 11
  loop : -1.14 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.025   0.002   PHE A 454 
 TYR   0.010   0.001   TYR A  98 
 ARG   0.001   0.000   ARG A 630 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9334 (m-30) cc_final: 0.8860 (m-30)
REVERT: A   38 TYR cc_start: 0.8190 (m-80) cc_final: 0.6590 (m-80)
REVERT: A   82 MET cc_start: 0.9138 (tpt) cc_final: 0.8880 (tpp)
REVERT: A  157 MET cc_start: 0.7806 (pmm) cc_final: 0.7425 (ptm)
REVERT: A  180 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8840 (tm-30)
REVERT: A  262 TYR cc_start: 0.9472 (m-80) cc_final: 0.8936 (m-80)
REVERT: A  320 MET cc_start: 0.8662 (tpp) cc_final: 0.8132 (ttt)
REVERT: A  378 MET cc_start: 0.8856 (mmp) cc_final: 0.8602 (mtt)
REVERT: A  437 PHE cc_start: 0.9142 (m-10) cc_final: 0.8304 (m-80)
REVERT: A  469 TYR cc_start: 0.9622 (t80) cc_final: 0.9268 (t80)
REVERT: A  476 VAL cc_start: 0.9303 (t) cc_final: 0.9093 (t)
REVERT: A  511 MET cc_start: 0.9142 (mmp) cc_final: 0.8882 (mmm)
REVERT: A  532 ILE cc_start: 0.9619 (tt) cc_final: 0.9039 (tt)
REVERT: A  533 LEU cc_start: 0.9389 (mm) cc_final: 0.8672 (mm)
REVERT: A  534 MET cc_start: 0.9478 (mpp) cc_final: 0.8985 (mpp)
REVERT: A  540 MET cc_start: 0.9609 (mmp) cc_final: 0.9290 (mmp)
REVERT: A  626 ASP cc_start: 0.8946 (m-30) cc_final: 0.8662 (m-30)
REVERT: A  682 ARG cc_start: 0.8579 (mpt-90) cc_final: 0.8053 (ttm110)
REVERT: A  710 ASN cc_start: 0.9203 (m-40) cc_final: 0.8985 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1302
  time to fit residues: 30.1255
Evaluate side-chains
  131 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5229  Z= 0.207
  Angle     :  0.628   7.707   7113  Z= 0.319
  Chirality :  0.041   0.177    801
  Planarity :  0.004   0.043    882
  Dihedral  :  4.202  19.219    680
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.36), residues: 624
  helix:  1.80 (0.26), residues: 425
  sheet: -1.78 (1.40), residues: 11
  loop : -1.12 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.021   0.002   PHE A 454 
 TYR   0.009   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A 158 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9345 (m-30) cc_final: 0.8900 (m-30)
REVERT: A   38 TYR cc_start: 0.8231 (m-80) cc_final: 0.7167 (m-80)
REVERT: A   82 MET cc_start: 0.9164 (tpt) cc_final: 0.8869 (tpp)
REVERT: A  157 MET cc_start: 0.7895 (pmm) cc_final: 0.7444 (ptm)
REVERT: A  180 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8853 (tm-30)
REVERT: A  262 TYR cc_start: 0.9488 (m-80) cc_final: 0.8947 (m-80)
REVERT: A  320 MET cc_start: 0.8762 (tpp) cc_final: 0.8189 (ttt)
REVERT: A  378 MET cc_start: 0.8885 (mmp) cc_final: 0.8493 (mtt)
REVERT: A  389 PHE cc_start: 0.9072 (m-80) cc_final: 0.8833 (m-80)
REVERT: A  437 PHE cc_start: 0.9112 (m-10) cc_final: 0.8198 (m-80)
REVERT: A  469 TYR cc_start: 0.9656 (t80) cc_final: 0.9218 (t80)
REVERT: A  476 VAL cc_start: 0.9334 (t) cc_final: 0.9131 (t)
REVERT: A  511 MET cc_start: 0.9178 (mmp) cc_final: 0.8916 (mmm)
REVERT: A  532 ILE cc_start: 0.9618 (tt) cc_final: 0.8979 (tt)
REVERT: A  534 MET cc_start: 0.9487 (mpp) cc_final: 0.9192 (mpp)
REVERT: A  540 MET cc_start: 0.9614 (mmp) cc_final: 0.9300 (mmp)
REVERT: A  579 LEU cc_start: 0.9750 (mt) cc_final: 0.9520 (mt)
REVERT: A  626 ASP cc_start: 0.8999 (m-30) cc_final: 0.8794 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1438
  time to fit residues: 33.7681
Evaluate side-chains
  136 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0040
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5229  Z= 0.180
  Angle     :  0.635   7.799   7113  Z= 0.322
  Chirality :  0.041   0.182    801
  Planarity :  0.004   0.044    882
  Dihedral  :  4.200  19.172    680
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.24 (0.35), residues: 624
  helix:  1.74 (0.26), residues: 425
  sheet: -1.70 (1.44), residues: 11
  loop : -1.16 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.019   0.001   PHE A  19 
 TYR   0.006   0.001   TYR A  98 
 ARG   0.004   0.000   ARG A 682 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9336 (m-30) cc_final: 0.8885 (m-30)
REVERT: A   38 TYR cc_start: 0.8196 (m-80) cc_final: 0.6647 (m-80)
REVERT: A   82 MET cc_start: 0.9142 (tpt) cc_final: 0.8849 (tpp)
REVERT: A  157 MET cc_start: 0.7718 (pmm) cc_final: 0.7461 (ptm)
REVERT: A  180 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8975 (tp30)
REVERT: A  262 TYR cc_start: 0.9487 (m-80) cc_final: 0.8939 (m-80)
REVERT: A  298 ILE cc_start: 0.9627 (mm) cc_final: 0.9395 (pt)
REVERT: A  320 MET cc_start: 0.8726 (tpp) cc_final: 0.8262 (ttt)
REVERT: A  351 GLU cc_start: 0.8771 (tt0) cc_final: 0.8559 (mm-30)
REVERT: A  396 VAL cc_start: 0.9593 (t) cc_final: 0.9375 (t)
REVERT: A  437 PHE cc_start: 0.9113 (m-10) cc_final: 0.8218 (m-80)
REVERT: A  445 LEU cc_start: 0.9771 (mt) cc_final: 0.9567 (mt)
REVERT: A  469 TYR cc_start: 0.9647 (t80) cc_final: 0.9220 (t80)
REVERT: A  476 VAL cc_start: 0.9316 (t) cc_final: 0.9102 (t)
REVERT: A  511 MET cc_start: 0.9152 (mmp) cc_final: 0.8915 (mmm)
REVERT: A  532 ILE cc_start: 0.9616 (tt) cc_final: 0.8886 (tt)
REVERT: A  533 LEU cc_start: 0.9405 (mm) cc_final: 0.8710 (mm)
REVERT: A  534 MET cc_start: 0.9477 (mpp) cc_final: 0.9037 (mpp)
REVERT: A  540 MET cc_start: 0.9613 (mmp) cc_final: 0.9294 (mmp)
REVERT: A  579 LEU cc_start: 0.9727 (mt) cc_final: 0.9502 (mt)
REVERT: A  626 ASP cc_start: 0.8945 (m-30) cc_final: 0.8741 (m-30)
REVERT: A  677 GLU cc_start: 0.8511 (pt0) cc_final: 0.8306 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1277
  time to fit residues: 29.0466
Evaluate side-chains
  130 residues out of total 546 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 36 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   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:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** 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 = 0.3316 r_free = 0.3316 target = 0.082691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.063495 restraints weight = 17305.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.066035 restraints weight = 9649.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.067704 restraints weight = 6407.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5229  Z= 0.175
  Angle     :  0.626   7.852   7113  Z= 0.316
  Chirality :  0.041   0.160    801
  Planarity :  0.004   0.043    882
  Dihedral  :  4.209  19.160    680
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.06 (0.35), residues: 624
  helix:  1.56 (0.26), residues: 430
  sheet: -1.69 (1.47), residues: 10
  loop : -1.22 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 331 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.020   0.002   PHE A 324 
 TYR   0.016   0.001   TYR A 712 
 ARG   0.002   0.000   ARG A 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1424.03 seconds
wall clock time: 26 minutes 41.40 seconds (1601.40 seconds total)