Starting phenix.real_space_refine
on Thu Sep 26 04:42:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/09_2024/7lig_23375.cif"
  }
  resolution = 2.9
  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=   0.002 sd=   0.050
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     120      5.16       5
     C    8000      2.51       5
     N    1940      2.21       5
     O    2088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 12148
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3023
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 9, 'TRANS': 371}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'DE3': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.54, per 1000 atoms: 0.54
  Number of scatterers: 12148
  At special positions: 0
  Unit cell: (114.33, 114.33, 92.7, 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     120     16.00
     O    2088      8.00
     N    1940      7.00
     C    8000      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: 3.13
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2928

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      82.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 31
      removed outlier: 4.013A  pdb=" N   HIS A  16 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 3.657A  pdb=" N   LYS A  47 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 75
      removed outlier: 3.600A  pdb=" N   SER A  55 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS A  74 " --> pdb=" O   CYS A  70 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 105
      removed outlier: 4.401A  pdb=" N   VAL A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 118
      removed outlier: 3.956A  pdb=" N   LEU A 109 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLU A 110 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 161
      removed outlier: 4.190A  pdb=" N   LYS A 129 " --> pdb=" O   PRO A 125 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   MET A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 3.912A  pdb=" N   LEU A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 247
      Proline residue:  A 216  - end of helix
      removed outlier: 3.512A  pdb=" N   GLY A 247 " --> pdb=" O   CYS A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 366
      removed outlier: 4.280A  pdb=" N   SER A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 337 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TYR A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 407
      removed outlier: 3.672A  pdb=" N   LEU A 379 " --> pdb=" O   PRO A 375 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 381 " --> pdb=" O   MET A 377 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ALA A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   HIS A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 4.072A  pdb=" N   VAL A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 411 through 416'
    Processing helix  chain 'A' and resid 418 through 433
      removed outlier: 3.823A  pdb=" N   GLN A 426 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 469
      removed outlier: 3.586A  pdb=" N   ASN A 469 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 31
    Processing helix  chain 'B' and resid 44 through 48
      removed outlier: 3.658A  pdb=" N   LYS B  47 " --> pdb=" O   ASN B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 75
      removed outlier: 3.600A  pdb=" N   SER B  55 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS B  74 " --> pdb=" O   CYS B  70 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B  75 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 105
      removed outlier: 4.401A  pdb=" N   VAL B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN B 105 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 118
      removed outlier: 3.957A  pdb=" N   LEU B 109 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR B 111 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 161
      removed outlier: 4.190A  pdb=" N   LYS B 129 " --> pdb=" O   PRO B 125 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   MET B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
      removed outlier: 3.913A  pdb=" N   LEU B 166 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 247
      Proline residue:  B 216  - end of helix
      removed outlier: 3.513A  pdb=" N   GLY B 247 " --> pdb=" O   CYS B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 366
      removed outlier: 4.278A  pdb=" N   SER B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   VAL B 341 " --> pdb=" O   ILE B 337 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 407
      removed outlier: 3.672A  pdb=" N   LEU B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 381 " --> pdb=" O   MET B 377 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ALA B 399 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
      removed outlier: 4.071A  pdb=" N   VAL B 415 " --> pdb=" O   SER B 411 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 416 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 411 through 416'
    Processing helix  chain 'B' and resid 418 through 433
      removed outlier: 3.823A  pdb=" N   GLN B 426 " --> pdb=" O   ARG B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 469
      removed outlier: 3.587A  pdb=" N   ASN B 469 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 31
    Processing helix  chain 'C' and resid 44 through 48
      removed outlier: 3.657A  pdb=" N   LYS C  47 " --> pdb=" O   ASN C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 75
      removed outlier: 3.600A  pdb=" N   SER C  55 " --> pdb=" O   ARG C  51 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   CYS C  74 " --> pdb=" O   CYS C  70 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C  75 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 105
      removed outlier: 4.401A  pdb=" N   VAL C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN C 105 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 118
      removed outlier: 3.956A  pdb=" N   LEU C 109 " --> pdb=" O   ASN C 105 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU C 110 " --> pdb=" O   SER C 106 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR C 111 " --> pdb=" O   ARG C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 161
      removed outlier: 4.190A  pdb=" N   LYS C 129 " --> pdb=" O   PRO C 125 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   MET C 130 " --> pdb=" O   ARG C 126 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER C 131 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 167
      removed outlier: 3.913A  pdb=" N   LEU C 166 " --> pdb=" O   PRO C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 247
      Proline residue:  C 216  - end of helix
      removed outlier: 3.513A  pdb=" N   GLY C 247 " --> pdb=" O   CYS C 243 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 366
      removed outlier: 4.279A  pdb=" N   SER C 340 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   VAL C 341 " --> pdb=" O   ILE C 337 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR C 342 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 407
      removed outlier: 3.672A  pdb=" N   LEU C 379 " --> pdb=" O   PRO C 375 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU C 381 " --> pdb=" O   MET C 377 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET C 382 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA C 399 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS C 407 " --> pdb=" O   LEU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 416
      removed outlier: 4.072A  pdb=" N   VAL C 415 " --> pdb=" O   SER C 411 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU C 416 " --> pdb=" O   SER C 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 411 through 416'
    Processing helix  chain 'C' and resid 418 through 433
      removed outlier: 3.823A  pdb=" N   GLN C 426 " --> pdb=" O   ARG C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 469
      removed outlier: 3.587A  pdb=" N   ASN C 469 " --> pdb=" O   LEU C 465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 31
    Processing helix  chain 'D' and resid 44 through 48
      removed outlier: 3.657A  pdb=" N   LYS D  47 " --> pdb=" O   ASN D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.600A  pdb=" N   SER D  55 " --> pdb=" O   ARG D  51 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS D  74 " --> pdb=" O   CYS D  70 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU D  75 " --> pdb=" O   ILE D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 105
      removed outlier: 4.401A  pdb=" N   VAL D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN D 105 " --> pdb=" O   SER D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 118
      removed outlier: 3.956A  pdb=" N   LEU D 109 " --> pdb=" O   ASN D 105 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU D 110 " --> pdb=" O   SER D 106 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR D 111 " --> pdb=" O   ARG D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 161
      removed outlier: 4.189A  pdb=" N   LYS D 129 " --> pdb=" O   PRO D 125 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   MET D 130 " --> pdb=" O   ARG D 126 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER D 131 " --> pdb=" O   GLY D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 167
      removed outlier: 3.913A  pdb=" N   LEU D 166 " --> pdb=" O   PRO D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 247
      Proline residue:  D 216  - end of helix
      removed outlier: 3.513A  pdb=" N   GLY D 247 " --> pdb=" O   CYS D 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 366
      removed outlier: 4.279A  pdb=" N   SER D 340 " --> pdb=" O   GLU D 336 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   VAL D 341 " --> pdb=" O   ILE D 337 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR D 342 " --> pdb=" O   VAL D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 373 through 407
      removed outlier: 3.671A  pdb=" N   LEU D 379 " --> pdb=" O   PRO D 375 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU D 381 " --> pdb=" O   MET D 377 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET D 382 " --> pdb=" O   VAL D 378 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL D 398 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA D 399 " --> pdb=" O   ALA D 395 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   HIS D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 416
      removed outlier: 4.072A  pdb=" N   VAL D 415 " --> pdb=" O   SER D 411 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU D 416 " --> pdb=" O   SER D 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 411 through 416'
    Processing helix  chain 'D' and resid 418 through 433
      removed outlier: 3.823A  pdb=" N   GLN D 426 " --> pdb=" O   ARG D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 469
      removed outlier: 3.587A  pdb=" N   ASN D 469 " --> pdb=" O   LEU D 465 " (cutoff:3.500A)

    928 hydrogen bonds defined for protein.
    2772 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: 3.46

  Time building geometry restraints manager: 3.60 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1780
        1.31 -     1.43: 3527
        1.43 -     1.56: 6941
        1.56 -     1.68: 4
        1.68 -     1.81: 172
  Bond restraints: 12424
  Sorted by residual:
  bond pdb=" CAH DE3 D 900 "
       pdb=" NAM DE3 D 900 "
    ideal  model  delta    sigma   weight residual
    1.347  1.455 -0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" CAH DE3 C 900 "
       pdb=" NAM DE3 C 900 "
    ideal  model  delta    sigma   weight residual
    1.347  1.455 -0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" CAH DE3 B 900 "
       pdb=" NAM DE3 B 900 "
    ideal  model  delta    sigma   weight residual
    1.347  1.455 -0.108 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" CAH DE3 A 900 "
       pdb=" NAM DE3 A 900 "
    ideal  model  delta    sigma   weight residual
    1.347  1.454 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" CAH DE3 C 900 "
       pdb=" OAN DE3 C 900 "
    ideal  model  delta    sigma   weight residual
    1.226  1.180  0.046 2.00e-02 2.50e+03 5.25e+00
  ... (remaining 12419 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 15917
        1.60 -     3.20: 800
        3.20 -     4.81: 103
        4.81 -     6.41: 24
        6.41 -     8.01: 8
  Bond angle restraints: 16852
  Sorted by residual:
  angle pdb=" N   ALA C 215 "
        pdb=" CA  ALA C 215 "
        pdb=" C   ALA C 215 "
      ideal   model   delta    sigma   weight residual
     112.17  116.04   -3.87 1.36e+00 5.41e-01 8.09e+00
  angle pdb=" N   ALA A 215 "
        pdb=" CA  ALA A 215 "
        pdb=" C   ALA A 215 "
      ideal   model   delta    sigma   weight residual
     112.17  116.01   -3.84 1.36e+00 5.41e-01 7.99e+00
  angle pdb=" N   ALA D 215 "
        pdb=" CA  ALA D 215 "
        pdb=" C   ALA D 215 "
      ideal   model   delta    sigma   weight residual
     112.17  116.00   -3.83 1.36e+00 5.41e-01 7.94e+00
  angle pdb=" N   ALA B 215 "
        pdb=" CA  ALA B 215 "
        pdb=" C   ALA B 215 "
      ideal   model   delta    sigma   weight residual
     112.17  115.97   -3.80 1.36e+00 5.41e-01 7.81e+00
  angle pdb=" C   SER B 370 "
        pdb=" N   PHE B 371 "
        pdb=" CA  PHE B 371 "
      ideal   model   delta    sigma   weight residual
     121.54  126.75   -5.21 1.91e+00 2.74e-01 7.44e+00
  ... (remaining 16847 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 6404
       17.90 -    35.79: 676
       35.79 -    53.69: 152
       53.69 -    71.58: 32
       71.58 -    89.48: 16
  Dihedral angle restraints: 7280
    sinusoidal: 2772
      harmonic: 4508
  Sorted by residual:
  dihedral pdb=" CA  ALA A 365 "
           pdb=" C   ALA A 365 "
           pdb=" N   ALA A 366 "
           pdb=" CA  ALA A 366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ALA C 365 "
           pdb=" C   ALA C 365 "
           pdb=" N   ALA C 366 "
           pdb=" CA  ALA C 366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ALA D 365 "
           pdb=" C   ALA D 365 "
           pdb=" N   ALA D 366 "
           pdb=" CA  ALA D 366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.02  -16.98     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 7277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1125
       0.030 -    0.059: 554
       0.059 -    0.089: 219
       0.089 -    0.118: 80
       0.118 -    0.148: 38
  Chirality restraints: 2016
  Sorted by residual:
  chirality pdb=" CG  LEU C 349 "
            pdb=" CB  LEU C 349 "
            pdb=" CD1 LEU C 349 "
            pdb=" CD2 LEU C 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CG  LEU D 349 "
            pdb=" CB  LEU D 349 "
            pdb=" CD1 LEU D 349 "
            pdb=" CD2 LEU D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" CG  LEU B 349 "
            pdb=" CB  LEU B 349 "
            pdb=" CD1 LEU B 349 "
            pdb=" CD2 LEU B 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 2013 not shown)

  Planarity restraints: 2020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 195 "    0.053 5.00e-02 4.00e+02   7.89e-02 9.96e+00
        pdb=" N   PRO D 196 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO D 196 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO D 196 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 195 "    0.052 5.00e-02 4.00e+02   7.87e-02 9.91e+00
        pdb=" N   PRO A 196 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 195 "   -0.052 5.00e-02 4.00e+02   7.87e-02 9.90e+00
        pdb=" N   PRO B 196 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO B 196 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 196 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 2017 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3999
        2.84 -     3.36: 12257
        3.36 -     3.87: 19632
        3.87 -     4.39: 21455
        4.39 -     4.90: 37560
  Nonbonded interactions: 94903
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 210 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   ILE D 210 "
            pdb=" OG1 THR D 214 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   ILE B 210 "
            pdb=" OG1 THR B 214 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   ILE C 210 "
            pdb=" OG1 THR C 214 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER D  31 "
            pdb=" OG  SER D  31 "
     model   vdw
     2.331 3.040
  ... (remaining 94898 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  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:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     28.270
  Find NCS groups from input model:        0.410
  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:12.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
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      :  0.006   0.108  12424  Z= 0.376
  Angle     :  0.801   8.010  16852  Z= 0.468
  Chirality :  0.044   0.148   2016
  Planarity :  0.008   0.079   2020
  Dihedral  : 16.002  89.477   4352
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.96 %
    Favored  : 90.56 %
  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: -1.68 (0.19), residues: 1500
  helix: -0.74 (0.13), residues: 1160
  sheet:  None (None), residues: 0
  loop : -1.91 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  20 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.023   0.002   PHE A 363 
 TYR   0.014   0.002   TYR A 380 
 ARG   0.003   0.000   ARG B  18 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 248
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 MET cc_start: 0.8284 (mtt) cc_final: 0.8051 (mtt)
REVERT: C  353 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (m)
REVERT: C  377 MET cc_start: 0.8390 (mtt) cc_final: 0.7883 (mtt)
REVERT: D  377 MET cc_start: 0.8326 (mtt) cc_final: 0.8062 (mtt)
  outliers start: 20
  outliers final: 4
  residues processed: 267
  average time/residue: 0.8531
  time to fit residues: 254.4112
Evaluate side-chains
  153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain B residue  343 SER
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  353 SER
Chi-restraints excluded: chain C residue  363 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 138 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 447 ASN
B 114 ASN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 ASN
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 114 ASN
D 447 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12424  Z= 0.206
  Angle     :  0.538   6.180  16852  Z= 0.288
  Chirality :  0.037   0.135   2016
  Planarity :  0.005   0.062   2020
  Dihedral  :  5.089  55.261   1662
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.29 %
    Favored  : 78.39 %
  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:  1.03 (0.22), residues: 1500
  helix:  1.18 (0.15), residues: 1180
  sheet:  None (None), residues: 0
  loop : -1.02 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  20 
 HIS   0.006   0.001   HIS A 233 
 PHE   0.024   0.001   PHE B 183 
 TYR   0.021   0.002   TYR B 204 
 ARG   0.002   0.000   ARG B  29 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 149
  time to evaluate  : 1.389 
Fit side-chains
REVERT: A   86 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7723 (tt)
REVERT: A  377 MET cc_start: 0.8054 (mtt) cc_final: 0.7574 (mtm)
REVERT: B  212 LEU cc_start: 0.8519 (mt) cc_final: 0.8277 (tt)
REVERT: B  377 MET cc_start: 0.8258 (mtt) cc_final: 0.7845 (mtm)
REVERT: C   86 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7519 (tt)
REVERT: D   86 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7630 (tt)
REVERT: D  377 MET cc_start: 0.8220 (mtt) cc_final: 0.7763 (mtm)
  outliers start: 45
  outliers final: 14
  residues processed: 171
  average time/residue: 0.8413
  time to fit residues: 162.0067
Evaluate side-chains
  151 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  363 PHE
Chi-restraints excluded: chain D residue  468 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:    0.4980
   chunk 114 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 138 optimal weight:    0.6980
   chunk 149 optimal weight:    0.2980
   chunk 123 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  16 HIS
A  52 GLN
B  45 GLN
B 447 ASN
C  16 HIS
D  16 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12424  Z= 0.176
  Angle     :  0.503   6.669  16852  Z= 0.267
  Chirality :  0.036   0.133   2016
  Planarity :  0.004   0.052   2020
  Dihedral  :  4.498  38.540   1656
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.76 %
    Favored  : 76.25 %
  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:  1.86 (0.22), residues: 1500
  helix:  1.78 (0.15), residues: 1180
  sheet:  None (None), residues: 0
  loop : -0.81 (0.39), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 187 
 HIS   0.007   0.001   HIS B  46 
 PHE   0.010   0.001   PHE B 223 
 TYR   0.018   0.001   TYR B 204 
 ARG   0.002   0.000   ARG A  18 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 1.309 
Fit side-chains
REVERT: A   86 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7538 (tt)
REVERT: A  190 PHE cc_start: 0.6935 (m-80) cc_final: 0.6713 (m-80)
REVERT: A  377 MET cc_start: 0.7998 (mtt) cc_final: 0.7555 (mtm)
REVERT: D  377 MET cc_start: 0.8199 (mtt) cc_final: 0.7768 (mtm)
  outliers start: 27
  outliers final: 7
  residues processed: 189
  average time/residue: 0.8093
  time to fit residues: 172.7043
Evaluate side-chains
  152 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  363 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain D residue  363 PHE
Chi-restraints excluded: chain D residue  468 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 138 optimal weight:    0.7980
   chunk 146 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 131 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  16 HIS
B  94 GLN
B 114 ASN
C  94 GLN
C 114 ASN
C 469 ASN
D 469 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12424  Z= 0.301
  Angle     :  0.573   6.824  16852  Z= 0.300
  Chirality :  0.039   0.184   2016
  Planarity :  0.004   0.041   2020
  Dihedral  :  4.469  42.567   1656
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.53 %
    Favored  : 75.15 %
  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:  2.10 (0.22), residues: 1500
  helix:  1.94 (0.15), residues: 1176
  sheet:  None (None), residues: 0
  loop : -0.60 (0.39), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  20 
 HIS   0.008   0.001   HIS B 233 
 PHE   0.013   0.001   PHE C 450 
 TYR   0.015   0.002   TYR B 204 
 ARG   0.002   0.000   ARG A  18 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 146
  time to evaluate  : 1.466 
Fit side-chains
REVERT: A   86 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7730 (tt)
REVERT: C  190 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6720 (m-80)
REVERT: D  182 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8210 (ptp90)
  outliers start: 45
  outliers final: 17
  residues processed: 168
  average time/residue: 0.8644
  time to fit residues: 163.6587
Evaluate side-chains
  153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  363 PHE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  348 THR
Chi-restraints excluded: chain D residue  468 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 125 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 131 optimal weight:    0.0030
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12424  Z= 0.192
  Angle     :  0.520   7.926  16852  Z= 0.272
  Chirality :  0.037   0.167   2016
  Planarity :  0.004   0.037   2020
  Dihedral  :  4.395  40.209   1656
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.38 %
    Favored  : 73.82 %
  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:  2.40 (0.23), residues: 1500
  helix:  2.14 (0.15), residues: 1184
  sheet:  None (None), residues: 0
  loop : -0.52 (0.40), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  34 
 HIS   0.007   0.001   HIS A 233 
 PHE   0.014   0.001   PHE B 223 
 TYR   0.020   0.001   TYR B 128 
 ARG   0.002   0.000   ARG B 387 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 1.408 
Fit side-chains
REVERT: A  377 MET cc_start: 0.7743 (mtm) cc_final: 0.7415 (mtm)
REVERT: B  454 MET cc_start: 0.6604 (ttt) cc_final: 0.6393 (ttt)
REVERT: C  190 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6638 (m-80)
REVERT: D  182 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8242 (ptp-170)
REVERT: D  377 MET cc_start: 0.7658 (mtm) cc_final: 0.7401 (mtm)
  outliers start: 38
  outliers final: 9
  residues processed: 177
  average time/residue: 0.8009
  time to fit residues: 160.6168
Evaluate side-chains
  148 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  363 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain D residue   24 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 132 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 147 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 469 ASN
B  94 GLN
C  94 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12424  Z= 0.197
  Angle     :  0.532   8.999  16852  Z= 0.275
  Chirality :  0.037   0.165   2016
  Planarity :  0.004   0.033   2020
  Dihedral  :  4.353  39.842   1656
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 24.85 %
    Favored  : 73.38 %
  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:  2.45 (0.23), residues: 1500
  helix:  2.17 (0.15), residues: 1184
  sheet:  None (None), residues: 0
  loop : -0.48 (0.40), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  20 
 HIS   0.008   0.001   HIS A 233 
 PHE   0.011   0.001   PHE A 363 
 TYR   0.019   0.001   TYR D 128 
 ARG   0.001   0.000   ARG C 387 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
REVERT: B  182 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8446 (ptp90)
REVERT: C  190 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6585 (m-80)
REVERT: C  407 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7647 (t-90)
REVERT: D  182 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8200 (ptp-170)
  outliers start: 24
  outliers final: 7
  residues processed: 161
  average time/residue: 0.9056
  time to fit residues: 163.2053
Evaluate side-chains
  146 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain C residue  407 HIS
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  468 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 123 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0040
   chunk 146 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0170
   chunk 89 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.4430

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12424  Z= 0.169
  Angle     :  0.555  10.810  16852  Z= 0.283
  Chirality :  0.037   0.163   2016
  Planarity :  0.003   0.032   2020
  Dihedral  :  4.343  38.709   1656
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 25.59 %
    Favored  : 73.45 %
  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:  2.53 (0.22), residues: 1500
  helix:  2.24 (0.15), residues: 1180
  sheet:  None (None), residues: 0
  loop : -0.48 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 155 
 HIS   0.009   0.001   HIS B 233 
 PHE   0.013   0.001   PHE A 363 
 TYR   0.023   0.001   TYR B 128 
 ARG   0.002   0.000   ARG C 373 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 1.450 
Fit side-chains
REVERT: A  377 MET cc_start: 0.7716 (mtm) cc_final: 0.7289 (mtm)
REVERT: B  182 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8341 (ptp90)
REVERT: B  190 PHE cc_start: 0.6684 (m-80) cc_final: 0.6411 (m-80)
REVERT: B  377 MET cc_start: 0.7701 (mtm) cc_final: 0.7375 (mtm)
REVERT: C  190 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6500 (m-80)
REVERT: D  182 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8210 (ptp-170)
  outliers start: 13
  outliers final: 6
  residues processed: 175
  average time/residue: 0.9218
  time to fit residues: 181.7063
Evaluate side-chains
  150 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  363 PHE
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain D residue   24 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 115 optimal weight:    0.3980
   chunk 133 optimal weight:    0.9980
   chunk 140 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 114 ASN
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12424  Z= 0.209
  Angle     :  0.570   9.631  16852  Z= 0.295
  Chirality :  0.037   0.165   2016
  Planarity :  0.003   0.033   2020
  Dihedral  :  4.365  40.156   1656
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 26.18 %
    Favored  : 72.71 %
  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:  2.48 (0.22), residues: 1500
  helix:  2.15 (0.15), residues: 1188
  sheet:  None (None), residues: 0
  loop : -0.32 (0.40), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  20 
 HIS   0.007   0.001   HIS B 233 
 PHE   0.023   0.001   PHE A 363 
 TYR   0.026   0.001   TYR B 128 
 ARG   0.002   0.000   ARG D 373 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 1.610 
Fit side-chains
REVERT: B  182 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8304 (ptp90)
REVERT: B  377 MET cc_start: 0.7688 (mtm) cc_final: 0.7408 (mtm)
REVERT: C  190 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6493 (m-80)
REVERT: D  182 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8205 (ptp90)
  outliers start: 15
  outliers final: 7
  residues processed: 159
  average time/residue: 0.9034
  time to fit residues: 160.3167
Evaluate side-chains
  146 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain D residue  184 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9990
   chunk 140 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 123 optimal weight:    0.5980
   chunk 129 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
** B  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12424  Z= 0.213
  Angle     :  0.582   9.322  16852  Z= 0.300
  Chirality :  0.038   0.175   2016
  Planarity :  0.003   0.033   2020
  Dihedral  :  4.389  40.703   1656
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 27.43 %
    Favored  : 71.90 %
  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:  2.51 (0.22), residues: 1500
  helix:  2.19 (0.15), residues: 1184
  sheet:  None (None), residues: 0
  loop : -0.35 (0.40), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  20 
 HIS   0.008   0.001   HIS B 233 
 PHE   0.016   0.001   PHE C 363 
 TYR   0.036   0.002   TYR D 128 
 ARG   0.002   0.000   ARG A 373 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 1.412 
Fit side-chains
REVERT: A  377 MET cc_start: 0.7682 (mtm) cc_final: 0.7198 (mtm)
REVERT: B  182 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8306 (ptp90)
REVERT: B  377 MET cc_start: 0.7628 (mtm) cc_final: 0.7373 (mtm)
REVERT: C  190 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6457 (m-80)
REVERT: D  377 MET cc_start: 0.7636 (mtm) cc_final: 0.7338 (mtm)
  outliers start: 9
  outliers final: 9
  residues processed: 151
  average time/residue: 0.9636
  time to fit residues: 162.1203
Evaluate side-chains
  147 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  468 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain D residue  184 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 151 optimal weight:    0.7980
   chunk 139 optimal weight:    0.8980
   chunk 120 optimal weight:    0.0670
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12424  Z= 0.188
  Angle     :  0.566   9.062  16852  Z= 0.294
  Chirality :  0.037   0.168   2016
  Planarity :  0.003   0.033   2020
  Dihedral  :  4.399  40.323   1656
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 27.58 %
    Favored  : 71.68 %
  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:  2.61 (0.22), residues: 1500
  helix:  2.26 (0.15), residues: 1184
  sheet:  None (None), residues: 0
  loop : -0.34 (0.40), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 155 
 HIS   0.008   0.001   HIS B 233 
 PHE   0.011   0.001   PHE B 223 
 TYR   0.036   0.002   TYR A 128 
 ARG   0.002   0.000   ARG D 373 

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 1.456 
Fit side-chains
REVERT: A  377 MET cc_start: 0.7573 (mtm) cc_final: 0.7096 (mtm)
REVERT: B  190 PHE cc_start: 0.6459 (m-80) cc_final: 0.6077 (m-80)
REVERT: C  190 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6250 (m-80)
REVERT: D  377 MET cc_start: 0.7586 (mtm) cc_final: 0.7329 (mtm)
  outliers start: 10
  outliers final: 7
  residues processed: 153
  average time/residue: 0.8818
  time to fit residues: 151.1668
Evaluate side-chains
  146 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 PHE
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain D residue  184 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0270
   chunk 22 optimal weight:    1.9990
   chunk 106 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6640

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.125579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.098255 restraints weight = 20843.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 3.39
r_work: 0.3270 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12424  Z= 0.198
  Angle     :  0.582   9.904  16852  Z= 0.300
  Chirality :  0.038   0.173   2016
  Planarity :  0.003   0.033   2020
  Dihedral  :  4.404  40.660   1656
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 27.43 %
    Favored  : 72.05 %
  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:  2.56 (0.22), residues: 1500
  helix:  2.24 (0.15), residues: 1180
  sheet:  None (None), residues: 0
  loop : -0.39 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 187 
 HIS   0.008   0.001   HIS B 233 
 PHE   0.014   0.001   PHE A 223 
 TYR   0.037   0.002   TYR B 128 
 ARG   0.003   0.000   ARG C 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3516.70 seconds
wall clock time: 64 minutes 43.65 seconds (3883.65 seconds total)