Starting phenix.real_space_refine
on Tue Jan 14 02:14:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_38727.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_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/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_38727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_38727.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_38727.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw1_38727/01_2025/8xw1_38727.cif"
  }
  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. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 3.36, per 1000 atoms: 0.66
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 666.9 milliseconds
  

  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: 0.53
  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: 1.60

  Time building geometry restraints manager: 2.25 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:
        0.00 -     1.58: 6746
        1.58 -     3.17: 287
        3.17 -     4.75: 55
        4.75 -     6.34: 20
        6.34 -     7.92: 5
  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 3.040
  nonbonded pdb=" OE1 GLU A  78 "
            pdb=" NZ  LYS A  81 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" O   PHE A 224 "
            pdb=" ND2 ASN A 228 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   TRP A 335 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   LEU A 635 "
            pdb=" OG  SER A 638 "
     model   vdw
     2.234 3.040
  ... (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:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.620
  Find NCS groups from input model:        0.060
  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:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.780
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.589 
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: 0.1378
  time to fit residues: 33.0306
Evaluate side-chains
  136 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 229 HIS
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.079644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.060225 restraints weight = 17817.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.062534 restraints weight = 10013.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.064280 restraints weight = 6781.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5229  Z= 0.238
  Angle     :  0.669   8.112   7113  Z= 0.341
  Chirality :  0.043   0.188    801
  Planarity :  0.005   0.037    882
  Dihedral  :  4.742  17.795    680
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  3.40 %
    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:  0.70 (0.35), residues: 624
  helix:  1.39 (0.25), residues: 422
  sheet: -2.04 (1.09), residues: 16
  loop : -1.46 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 236 
 PHE   0.029   0.002   PHE A 360 
 TYR   0.014   0.001   TYR A  98 
 ARG   0.007   0.001   ARG A 462 

*********************** 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 to be fit.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9288 (m-30) cc_final: 0.9009 (m-30)
REVERT: A   38 TYR cc_start: 0.8495 (m-80) cc_final: 0.7353 (m-80)
REVERT: A  178 MET cc_start: 0.9253 (ppp) cc_final: 0.9009 (ppp)
REVERT: A  180 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9116 (tp30)
REVERT: A  262 TYR cc_start: 0.9447 (m-80) cc_final: 0.9050 (m-80)
REVERT: A  309 ARG cc_start: 0.8887 (mmp80) cc_final: 0.8507 (mmp80)
REVERT: A  355 GLU cc_start: 0.9372 (tp30) cc_final: 0.9087 (tp30)
REVERT: A  368 TYR cc_start: 0.8783 (t80) cc_final: 0.8322 (t80)
REVERT: A  437 PHE cc_start: 0.8947 (m-80) cc_final: 0.8545 (m-80)
REVERT: A  461 GLU cc_start: 0.9281 (tp30) cc_final: 0.8682 (mm-30)
REVERT: A  475 ASN cc_start: 0.8999 (m110) cc_final: 0.8600 (m110)
REVERT: A  476 VAL cc_start: 0.9400 (t) cc_final: 0.9198 (t)
REVERT: A  511 MET cc_start: 0.9264 (mmp) cc_final: 0.8981 (mmm)
REVERT: A  540 MET cc_start: 0.9629 (mmp) cc_final: 0.9269 (mmp)
REVERT: A  576 TYR cc_start: 0.8701 (m-10) cc_final: 0.8484 (m-10)
REVERT: A  613 TYR cc_start: 0.9320 (m-80) cc_final: 0.8742 (m-80)
REVERT: A  661 LEU cc_start: 0.9792 (mt) cc_final: 0.9197 (mt)
REVERT: A  677 GLU cc_start: 0.8550 (pt0) cc_final: 0.8330 (pt0)
REVERT: A  689 MET cc_start: 0.9509 (mmp) cc_final: 0.9273 (mmm)
REVERT: A  690 MET cc_start: 0.9367 (mmt) cc_final: 0.9007 (tpt)
REVERT: A  710 ASN cc_start: 0.9443 (m-40) cc_final: 0.9240 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 0.1490
  time to fit residues: 36.2438
Evaluate side-chains
  142 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.080417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.060702 restraints weight = 17759.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.063167 restraints weight = 9908.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.064931 restraints weight = 6608.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5229  Z= 0.200
  Angle     :  0.658  12.807   7113  Z= 0.330
  Chirality :  0.042   0.179    801
  Planarity :  0.005   0.039    882
  Dihedral  :  4.549  17.373    680
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.40 %
    Favored  : 96.41 %
  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:  1.00 (0.35), residues: 624
  helix:  1.61 (0.26), residues: 422
  sheet: -1.74 (1.16), residues: 16
  loop : -1.32 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 624 
 HIS   0.006   0.001   HIS A 162 
 PHE   0.023   0.002   PHE A 717 
 TYR   0.010   0.001   TYR A 712 
 ARG   0.005   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
  178 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9300 (m-30) cc_final: 0.8953 (m-30)
REVERT: A  178 MET cc_start: 0.9219 (ppp) cc_final: 0.8953 (ppp)
REVERT: A  262 TYR cc_start: 0.9474 (m-80) cc_final: 0.9250 (m-80)
REVERT: A  355 GLU cc_start: 0.9370 (tp30) cc_final: 0.9040 (tp30)
REVERT: A  378 MET cc_start: 0.8986 (mmp) cc_final: 0.8782 (mmm)
REVERT: A  399 LEU cc_start: 0.9729 (mt) cc_final: 0.9524 (mt)
REVERT: A  437 PHE cc_start: 0.9012 (m-80) cc_final: 0.8488 (m-80)
REVERT: A  440 PHE cc_start: 0.8730 (m-10) cc_final: 0.8477 (t80)
REVERT: A  461 GLU cc_start: 0.9304 (tp30) cc_final: 0.8665 (mm-30)
REVERT: A  511 MET cc_start: 0.9284 (mmp) cc_final: 0.8987 (mmm)
REVERT: A  540 MET cc_start: 0.9625 (mmp) cc_final: 0.9261 (mmp)
REVERT: A  579 LEU cc_start: 0.9678 (mt) cc_final: 0.9371 (mt)
REVERT: A  613 TYR cc_start: 0.9306 (m-80) cc_final: 0.8701 (m-80)
REVERT: A  682 ARG cc_start: 0.8635 (mtt90) cc_final: 0.8407 (mtp85)
REVERT: A  689 MET cc_start: 0.9532 (mmp) cc_final: 0.9279 (mmm)
REVERT: A  690 MET cc_start: 0.9393 (mmt) cc_final: 0.9035 (tpt)
REVERT: A  710 ASN cc_start: 0.9419 (m-40) cc_final: 0.9199 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1361
  time to fit residues: 32.3708
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.080188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.060839 restraints weight = 18018.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.063351 restraints weight = 9813.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.064895 restraints weight = 6436.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2494

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     :  0.613   7.732   7113  Z= 0.316
  Chirality :  0.041   0.178    801
  Planarity :  0.004   0.039    882
  Dihedral  :  4.410  17.521    680
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.59 %
    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:  1.11 (0.35), residues: 624
  helix:  1.68 (0.25), residues: 421
  sheet: -1.96 (1.33), residues: 11
  loop : -1.25 (0.49), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.020   0.002   PHE A 428 
 TYR   0.008   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A 158 

*********************** 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
  170 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9329 (m-30) cc_final: 0.8969 (m-30)
REVERT: A  178 MET cc_start: 0.9195 (ppp) cc_final: 0.8881 (ppp)
REVERT: A  180 GLU cc_start: 0.9119 (tp30) cc_final: 0.8679 (tp30)
REVERT: A  355 GLU cc_start: 0.9382 (tp30) cc_final: 0.8871 (tp30)
REVERT: A  437 PHE cc_start: 0.9055 (m-80) cc_final: 0.8485 (m-80)
REVERT: A  441 LEU cc_start: 0.9806 (tt) cc_final: 0.9582 (tt)
REVERT: A  445 LEU cc_start: 0.9773 (mt) cc_final: 0.9525 (mt)
REVERT: A  461 GLU cc_start: 0.9329 (tp30) cc_final: 0.8953 (tp30)
REVERT: A  511 MET cc_start: 0.9313 (mmp) cc_final: 0.9005 (mmm)
REVERT: A  540 MET cc_start: 0.9624 (mmp) cc_final: 0.9272 (mmp)
REVERT: A  613 TYR cc_start: 0.9285 (m-80) cc_final: 0.8592 (m-80)
REVERT: A  677 GLU cc_start: 0.8649 (pt0) cc_final: 0.8421 (pt0)
REVERT: A  682 ARG cc_start: 0.8633 (mtt90) cc_final: 0.8282 (mtp85)
REVERT: A  689 MET cc_start: 0.9495 (mmp) cc_final: 0.9249 (mmm)
REVERT: A  690 MET cc_start: 0.9369 (mmt) cc_final: 0.9010 (tpt)
REVERT: A  710 ASN cc_start: 0.9383 (m-40) cc_final: 0.9159 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1379
  time to fit residues: 31.8989
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0470
   chunk 2 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
A 363 ASN
A 397 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.081507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.062788 restraints weight = 17430.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.065357 restraints weight = 9305.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.067180 restraints weight = 6021.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5229  Z= 0.177
  Angle     :  0.604   7.558   7113  Z= 0.307
  Chirality :  0.041   0.177    801
  Planarity :  0.004   0.046    882
  Dihedral  :  4.353  18.486    680
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  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:  1.04 (0.35), residues: 624
  helix:  1.60 (0.26), residues: 429
  sheet: -1.85 (1.33), residues: 11
  loop : -1.33 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.018   0.001   PHE A 428 
 TYR   0.008   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A 198 

*********************** 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
  176 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9292 (m-30) cc_final: 0.8916 (m-30)
REVERT: A   82 MET cc_start: 0.9159 (tpt) cc_final: 0.8925 (tpp)
REVERT: A  178 MET cc_start: 0.9186 (ppp) cc_final: 0.8838 (ppp)
REVERT: A  180 GLU cc_start: 0.9105 (tp30) cc_final: 0.8698 (tp30)
REVERT: A  262 TYR cc_start: 0.9442 (m-80) cc_final: 0.9134 (m-80)
REVERT: A  297 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9062 (mm-30)
REVERT: A  298 ILE cc_start: 0.9679 (mm) cc_final: 0.9477 (pt)
REVERT: A  399 LEU cc_start: 0.9721 (mt) cc_final: 0.9408 (mt)
REVERT: A  437 PHE cc_start: 0.9054 (m-80) cc_final: 0.8188 (m-80)
REVERT: A  445 LEU cc_start: 0.9774 (mt) cc_final: 0.9569 (mt)
REVERT: A  452 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7558 (mt-10)
REVERT: A  461 GLU cc_start: 0.9317 (tp30) cc_final: 0.9115 (mm-30)
REVERT: A  469 TYR cc_start: 0.9606 (t80) cc_final: 0.9332 (t80)
REVERT: A  511 MET cc_start: 0.9265 (mmp) cc_final: 0.8964 (mmm)
REVERT: A  540 MET cc_start: 0.9593 (mmp) cc_final: 0.9264 (mmp)
REVERT: A  677 GLU cc_start: 0.8623 (pt0) cc_final: 0.8387 (pt0)
REVERT: A  682 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8188 (mtp85)
REVERT: A  689 MET cc_start: 0.9483 (mmp) cc_final: 0.9263 (mmm)
REVERT: A  710 ASN cc_start: 0.9363 (m-40) cc_final: 0.9125 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1257
  time to fit residues: 30.2048
Evaluate side-chains
  135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.081769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.063335 restraints weight = 17119.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.065892 restraints weight = 9219.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.067623 restraints weight = 5955.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5229  Z= 0.170
  Angle     :  0.603   7.892   7113  Z= 0.304
  Chirality :  0.041   0.180    801
  Planarity :  0.004   0.045    882
  Dihedral  :  4.163  18.322    680
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.27 %
    Favored  : 97.54 %
  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:  1.58 (0.25), residues: 435
  sheet: -1.77 (1.33), residues: 11
  loop : -1.32 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  75 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.017   0.001   PHE A 428 
 TYR   0.010   0.001   TYR A  98 
 ARG   0.003   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
  171 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9281 (m-30) cc_final: 0.8889 (m-30)
REVERT: A   82 MET cc_start: 0.9203 (tpt) cc_final: 0.8946 (tpt)
REVERT: A  178 MET cc_start: 0.9180 (ppp) cc_final: 0.8886 (ppp)
REVERT: A  180 GLU cc_start: 0.9122 (tp30) cc_final: 0.8705 (tp30)
REVERT: A  262 TYR cc_start: 0.9455 (m-80) cc_final: 0.9103 (m-80)
REVERT: A  298 ILE cc_start: 0.9658 (mm) cc_final: 0.9439 (pt)
REVERT: A  437 PHE cc_start: 0.9081 (m-80) cc_final: 0.8181 (m-80)
REVERT: A  445 LEU cc_start: 0.9763 (mt) cc_final: 0.9562 (mt)
REVERT: A  452 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7529 (mt-10)
REVERT: A  461 GLU cc_start: 0.9308 (tp30) cc_final: 0.8961 (tp30)
REVERT: A  469 TYR cc_start: 0.9623 (t80) cc_final: 0.9292 (t80)
REVERT: A  511 MET cc_start: 0.9242 (mmp) cc_final: 0.8915 (mmm)
REVERT: A  540 MET cc_start: 0.9606 (mmp) cc_final: 0.9279 (mmp)
REVERT: A  579 LEU cc_start: 0.9701 (mt) cc_final: 0.9496 (mt)
REVERT: A  613 TYR cc_start: 0.8993 (m-80) cc_final: 0.8474 (m-80)
REVERT: A  682 ARG cc_start: 0.8465 (mtt90) cc_final: 0.8087 (mtp85)
REVERT: A  710 ASN cc_start: 0.9342 (m-40) cc_final: 0.9116 (m-40)
  outliers start: 1
  outliers final: 1
  residues processed: 171
  average time/residue: 0.1315
  time to fit residues: 30.9847
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 22 optimal weight:   30.0000
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.3980
   chunk 27 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.082040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.062623 restraints weight = 17400.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.065119 restraints weight = 9719.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.066922 restraints weight = 6450.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5229  Z= 0.191
  Angle     :  0.621   7.943   7113  Z= 0.316
  Chirality :  0.041   0.177    801
  Planarity :  0.004   0.046    882
  Dihedral  :  4.197  17.531    680
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  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 (0.35), residues: 624
  helix:  1.64 (0.26), residues: 432
  sheet: -1.68 (1.33), residues: 11
  loop : -1.12 (0.49), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  75 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.017   0.001   PHE A 428 
 TYR   0.010   0.001   TYR A 613 
 ARG   0.002   0.000   ARG A 158 

*********************** 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
  166 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9264 (m-30) cc_final: 0.8881 (m-30)
REVERT: A   82 MET cc_start: 0.9199 (tpt) cc_final: 0.8929 (tpt)
REVERT: A   97 VAL cc_start: 0.9692 (t) cc_final: 0.9445 (p)
REVERT: A  165 MET cc_start: 0.9475 (mmp) cc_final: 0.9182 (mmp)
REVERT: A  180 GLU cc_start: 0.9157 (tp30) cc_final: 0.8773 (tp30)
REVERT: A  262 TYR cc_start: 0.9468 (m-80) cc_final: 0.8911 (m-80)
REVERT: A  298 ILE cc_start: 0.9623 (mm) cc_final: 0.9387 (pt)
REVERT: A  437 PHE cc_start: 0.9090 (m-80) cc_final: 0.8189 (m-80)
REVERT: A  445 LEU cc_start: 0.9759 (mt) cc_final: 0.9541 (mt)
REVERT: A  452 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7596 (mt-10)
REVERT: A  461 GLU cc_start: 0.9294 (tp30) cc_final: 0.8925 (tp30)
REVERT: A  469 TYR cc_start: 0.9617 (t80) cc_final: 0.9143 (t80)
REVERT: A  511 MET cc_start: 0.9218 (mmp) cc_final: 0.8898 (mmm)
REVERT: A  540 MET cc_start: 0.9616 (mmp) cc_final: 0.9284 (mmp)
REVERT: A  579 LEU cc_start: 0.9708 (mt) cc_final: 0.9413 (mt)
REVERT: A  613 TYR cc_start: 0.9056 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  689 MET cc_start: 0.9325 (mmt) cc_final: 0.9088 (mmm)
REVERT: A  690 MET cc_start: 0.9511 (mtm) cc_final: 0.9161 (ptp)
REVERT: A  710 ASN cc_start: 0.9343 (m-40) cc_final: 0.9129 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1282
  time to fit residues: 29.2651
Evaluate side-chains
  130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.3322

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.082168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.062825 restraints weight = 17614.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.065426 restraints weight = 9638.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.067178 restraints weight = 6322.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5229  Z= 0.192
  Angle     :  0.610   7.506   7113  Z= 0.312
  Chirality :  0.041   0.180    801
  Planarity :  0.005   0.048    882
  Dihedral  :  4.175  17.058    680
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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:  1.31 (0.35), residues: 624
  helix:  1.77 (0.26), residues: 425
  sheet: -1.63 (1.32), residues: 11
  loop : -1.09 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  75 
 HIS   0.008   0.001   HIS A 628 
 PHE   0.027   0.002   PHE A 668 
 TYR   0.008   0.001   TYR A 613 
 ARG   0.002   0.000   ARG A 158 

*********************** 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
  167 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9282 (m-30) cc_final: 0.8884 (m-30)
REVERT: A   82 MET cc_start: 0.9218 (tpt) cc_final: 0.8935 (tpt)
REVERT: A   97 VAL cc_start: 0.9705 (t) cc_final: 0.9468 (p)
REVERT: A  165 MET cc_start: 0.9456 (mmp) cc_final: 0.9183 (mmp)
REVERT: A  180 GLU cc_start: 0.9143 (tp30) cc_final: 0.8784 (tp30)
REVERT: A  262 TYR cc_start: 0.9474 (m-80) cc_final: 0.8924 (m-80)
REVERT: A  320 MET cc_start: 0.8846 (tpt) cc_final: 0.8544 (ttt)
REVERT: A  437 PHE cc_start: 0.9100 (m-10) cc_final: 0.8201 (m-80)
REVERT: A  445 LEU cc_start: 0.9780 (mt) cc_final: 0.9575 (mt)
REVERT: A  452 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7530 (mt-10)
REVERT: A  461 GLU cc_start: 0.9287 (tp30) cc_final: 0.8910 (tp30)
REVERT: A  469 TYR cc_start: 0.9630 (t80) cc_final: 0.9184 (t80)
REVERT: A  511 MET cc_start: 0.9239 (mmp) cc_final: 0.8913 (mmm)
REVERT: A  540 MET cc_start: 0.9622 (mmp) cc_final: 0.9285 (mmp)
REVERT: A  579 LEU cc_start: 0.9713 (mt) cc_final: 0.9394 (mt)
REVERT: A  613 TYR cc_start: 0.9085 (m-80) cc_final: 0.8364 (m-80)
REVERT: A  689 MET cc_start: 0.9294 (mmt) cc_final: 0.9061 (mmm)
REVERT: A  690 MET cc_start: 0.9478 (mtm) cc_final: 0.9123 (ptp)
REVERT: A  710 ASN cc_start: 0.9354 (m-40) cc_final: 0.9143 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1332
  time to fit residues: 30.3468
Evaluate side-chains
  131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.081703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.062477 restraints weight = 17440.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.064990 restraints weight = 9667.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.066801 restraints weight = 6402.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5229  Z= 0.198
  Angle     :  0.623   8.055   7113  Z= 0.319
  Chirality :  0.042   0.177    801
  Planarity :  0.005   0.049    882
  Dihedral  :  4.139  17.278    680
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    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:  1.20 (0.35), residues: 624
  helix:  1.63 (0.25), residues: 431
  sheet: -1.49 (1.48), residues: 10
  loop : -1.08 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  75 
 HIS   0.008   0.001   HIS A 628 
 PHE   0.029   0.002   PHE A 668 
 TYR   0.008   0.001   TYR A 613 
 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
  165 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9268 (m-30) cc_final: 0.8881 (m-30)
REVERT: A   38 TYR cc_start: 0.8581 (m-80) cc_final: 0.7466 (m-80)
REVERT: A   82 MET cc_start: 0.9200 (tpt) cc_final: 0.8944 (tpt)
REVERT: A   97 VAL cc_start: 0.9703 (t) cc_final: 0.9462 (p)
REVERT: A  178 MET cc_start: 0.9216 (ppp) cc_final: 0.8888 (ppp)
REVERT: A  180 GLU cc_start: 0.9142 (tp30) cc_final: 0.8782 (tp30)
REVERT: A  262 TYR cc_start: 0.9478 (m-80) cc_final: 0.8928 (m-80)
REVERT: A  320 MET cc_start: 0.8862 (tpt) cc_final: 0.8593 (ttt)
REVERT: A  437 PHE cc_start: 0.9092 (m-10) cc_final: 0.8184 (m-80)
REVERT: A  448 MET cc_start: 0.9472 (tpt) cc_final: 0.9206 (tpt)
REVERT: A  452 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7481 (mt-10)
REVERT: A  461 GLU cc_start: 0.9273 (tp30) cc_final: 0.8900 (tp30)
REVERT: A  469 TYR cc_start: 0.9664 (t80) cc_final: 0.9141 (t80)
REVERT: A  511 MET cc_start: 0.9234 (mmp) cc_final: 0.8907 (mmm)
REVERT: A  532 ILE cc_start: 0.9540 (tt) cc_final: 0.9312 (tt)
REVERT: A  533 LEU cc_start: 0.9549 (mm) cc_final: 0.8933 (mm)
REVERT: A  540 MET cc_start: 0.9610 (mmp) cc_final: 0.9273 (mmp)
REVERT: A  579 LEU cc_start: 0.9738 (mt) cc_final: 0.9406 (mt)
REVERT: A  677 GLU cc_start: 0.8614 (pt0) cc_final: 0.8356 (pt0)
REVERT: A  689 MET cc_start: 0.9275 (mmt) cc_final: 0.9011 (mmm)
REVERT: A  710 ASN cc_start: 0.9329 (m-40) cc_final: 0.9110 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1364
  time to fit residues: 30.8115
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:    0.0020
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.083965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.064428 restraints weight = 17283.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.067007 restraints weight = 9628.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.068804 restraints weight = 6369.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5229  Z= 0.184
  Angle     :  0.659   8.499   7113  Z= 0.332
  Chirality :  0.042   0.181    801
  Planarity :  0.005   0.050    882
  Dihedral  :  4.135  17.572    680
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  1.55 (0.25), residues: 436
  sheet: -1.38 (1.48), residues: 10
  loop : -1.30 (0.47), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  75 
 HIS   0.007   0.001   HIS A 628 
 PHE   0.031   0.002   PHE A 668 
 TYR   0.007   0.001   TYR A  98 
 ARG   0.005   0.000   ARG A 309 

********************** 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
  170 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9251 (m-30) cc_final: 0.8518 (t0)
REVERT: A   38 TYR cc_start: 0.8480 (m-80) cc_final: 0.7590 (m-80)
REVERT: A   82 MET cc_start: 0.9152 (tpt) cc_final: 0.8942 (tpt)
REVERT: A   98 TYR cc_start: 0.8809 (t80) cc_final: 0.8567 (t80)
REVERT: A  165 MET cc_start: 0.9412 (mmp) cc_final: 0.9153 (mmp)
REVERT: A  178 MET cc_start: 0.9190 (ppp) cc_final: 0.8910 (tmm)
REVERT: A  180 GLU cc_start: 0.9077 (tp30) cc_final: 0.8738 (tp30)
REVERT: A  262 TYR cc_start: 0.9481 (m-80) cc_final: 0.8924 (m-80)
REVERT: A  298 ILE cc_start: 0.9588 (mm) cc_final: 0.9304 (pt)
REVERT: A  358 ASP cc_start: 0.8996 (t0) cc_final: 0.8579 (t0)
REVERT: A  424 VAL cc_start: 0.9231 (m) cc_final: 0.8969 (p)
REVERT: A  437 PHE cc_start: 0.9086 (m-10) cc_final: 0.8184 (m-80)
REVERT: A  445 LEU cc_start: 0.9705 (mt) cc_final: 0.9484 (mt)
REVERT: A  448 MET cc_start: 0.9452 (tpt) cc_final: 0.9206 (tpt)
REVERT: A  452 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7507 (mt-10)
REVERT: A  461 GLU cc_start: 0.9268 (tp30) cc_final: 0.8934 (tp30)
REVERT: A  469 TYR cc_start: 0.9641 (t80) cc_final: 0.9118 (t80)
REVERT: A  511 MET cc_start: 0.9202 (mmp) cc_final: 0.8865 (mmm)
REVERT: A  532 ILE cc_start: 0.9531 (tt) cc_final: 0.9311 (tt)
REVERT: A  533 LEU cc_start: 0.9528 (mm) cc_final: 0.8904 (mm)
REVERT: A  540 MET cc_start: 0.9607 (mmp) cc_final: 0.9259 (mmp)
REVERT: A  579 LEU cc_start: 0.9730 (mt) cc_final: 0.9412 (mt)
REVERT: A  613 TYR cc_start: 0.8885 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  677 GLU cc_start: 0.8549 (pt0) cc_final: 0.8268 (pt0)
REVERT: A  689 MET cc_start: 0.9213 (mmt) cc_final: 0.9006 (mmm)
REVERT: A  710 ASN cc_start: 0.9318 (m-40) cc_final: 0.9046 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1234
  time to fit residues: 28.8866
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0570
   chunk 36 optimal weight:    0.0050
   chunk 55 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.5314

-------------------------------------------------------------------------------
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 397 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.083943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.064384 restraints weight = 17214.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.066998 restraints weight = 9658.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.068890 restraints weight = 6428.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3805

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= 0.185
  Angle     :  0.648   8.086   7113  Z= 0.332
  Chirality :  0.042   0.184    801
  Planarity :  0.004   0.049    882
  Dihedral  :  4.173  17.389    680
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  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:  1.05 (0.35), residues: 624
  helix:  1.52 (0.26), residues: 431
  sheet: -1.26 (1.47), residues: 10
  loop : -1.17 (0.47), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  75 
 HIS   0.007   0.001   HIS A 628 
 PHE   0.029   0.002   PHE A 324 
 TYR   0.015   0.001   TYR A 712 
 ARG   0.002   0.000   ARG A 188 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1786.83 seconds
wall clock time: 34 minutes 0.03 seconds (2040.03 seconds total)