Starting phenix.real_space_refine
on Thu Mar 13 01:54:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmg_22258/03_2025/6xmg_22258.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     154      5.49       5
     S      11      5.16       5
     C    4674      2.51       5
     N    1553      2.21       5
     O    1968      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8361
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 638, 5081
          Classifications: {'peptide': 638}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 38, 'TRANS': 599}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 266
          Unresolved non-hydrogen dihedrals: 187
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 139
    Chain: "C"
      Number of atoms: 2772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2772
          Classifications: {'RNA': 130}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 56}
          Link IDs: {'rna2p': 15, 'rna3p': 114}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 507
          Classifications: {'RNA': 24}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 13}
          Link IDs: {'rna3p': 23}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4654  SG  CYS A 714      51.688  83.830  49.919  1.00352.65           S

  Time building chain proxies: 5.34, per 1000 atoms: 0.64
  Number of scatterers: 8361
  At special positions: 0
  Unit cell: (106.05, 94.5, 132.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      11     16.00
     P     154     15.00
     O    1968      8.00
     N    1553      7.00
     C    4674      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: 2.17
  Conformation dependent library (CDL) restraints added in 637.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 714 "


  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 4 sheets defined
      49.4% alpha, 5.8% beta
      43 base pairs and 104 stacking pairs defined.
    Time for finding SS restraints: 4.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 65
      removed outlier: 3.637A  pdb=" N   ALA A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A  62 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 78 through 87
      removed outlier: 3.754A  pdb=" N   TRP A  82 " --> pdb=" O   THR A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.970A  pdb=" N   SER A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 3.622A  pdb=" N   ARG A 104 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.818A  pdb=" N   SER A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 153
    Processing helix  chain 'A' and resid 156 through 175
      removed outlier: 3.518A  pdb=" N   LYS A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 174 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 200
      removed outlier: 3.892A  pdb=" N   GLN A 198 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 214
      removed outlier: 3.540A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
    Processing helix  chain 'A' and resid 242 through 249
    Processing helix  chain 'A' and resid 336 through 347
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 4.565A  pdb=" N   LYS A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 3.669A  pdb=" N   THR A 434 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.741A  pdb=" N   LEU A 470 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 483 through 499
      removed outlier: 3.723A  pdb=" N   PHE A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 495 " --> pdb=" O   ALA A 491 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A 497 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR A 498 " --> pdb=" O   ARG A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 569 through 595
      removed outlier: 3.804A  pdb=" N   HIS A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA A 582 " --> pdb=" O   GLN A 578 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 595 " --> pdb=" O   ARG A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 644
      removed outlier: 3.593A  pdb=" N   ILE A 641 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.660A  pdb=" N   ARG A 685 " --> pdb=" O   HIS A 681 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ARG A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 693 " --> pdb=" O   THR A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 731
      removed outlier: 4.009A  pdb=" N   ARG A 730 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 757
      removed outlier: 3.630A  pdb=" N   TRP A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26
      removed outlier: 3.685A  pdb=" N   ARG A  26 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 450 " --> pdb=" O   ARG A  26 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER A 438 " --> pdb=" O   ARG A 453 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU A 441 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 511
      removed outlier: 3.564A  pdb=" N   VAL A 653 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE A 652 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524
      removed outlier: 6.725A  pdb=" N   ALA A 521 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   PHE A 523 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    195 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      99 hydrogen bonds
      194 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      104 stacking parallelities
  Total time for adding SS restraints: 3.41

  Time building geometry restraints manager: 2.58 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: 1025
        1.31 -     1.43: 3323
        1.43 -     1.56: 4192
        1.56 -     1.69: 305
        1.69 -     1.81: 16
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" C   ARG A 675 "
       pdb=" O   ARG A 675 "
    ideal  model  delta    sigma   weight residual
    1.233  1.180  0.052 1.09e-02 8.42e+03 2.31e+01
  bond pdb=" C   ARG A 675 "
       pdb=" N   VAL A 676 "
    ideal  model  delta    sigma   weight residual
    1.332  1.305  0.026 1.36e-02 5.41e+03 3.79e+00
  bond pdb=" CA  ILE A 766 "
       pdb=" CB  ILE A 766 "
    ideal  model  delta    sigma   weight residual
    1.539  1.530  0.009 5.40e-03 3.43e+04 2.68e+00
  bond pdb=" N   ARG A 675 "
       pdb=" CA  ARG A 675 "
    ideal  model  delta    sigma   weight residual
    1.463  1.482 -0.019 1.29e-02 6.01e+03 2.15e+00
  bond pdb=" N   LYS A 551 "
       pdb=" CA  LYS A 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.27e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 12399
        1.49 -     2.98: 263
        2.98 -     4.47: 40
        4.47 -     5.95: 11
        5.95 -     7.44: 1
  Bond angle restraints: 12714
  Sorted by residual:
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" CB  PRO A 229 "
      ideal   model   delta    sigma   weight residual
     103.00  110.44   -7.44 1.10e+00 8.26e-01 4.58e+01
  angle pdb=" C3'   A C 113 "
        pdb=" O3'   A C 113 "
        pdb=" P     A C 114 "
      ideal   model   delta    sigma   weight residual
     120.20  125.64   -5.44 1.50e+00 4.44e-01 1.32e+01
  angle pdb=" N   GLN A 552 "
        pdb=" CA  GLN A 552 "
        pdb=" C   GLN A 552 "
      ideal   model   delta    sigma   weight residual
     107.73  112.27   -4.54 1.34e+00 5.57e-01 1.15e+01
  angle pdb=" C   LEU A 203 "
        pdb=" N   THR A 204 "
        pdb=" CA  THR A 204 "
      ideal   model   delta    sigma   weight residual
     122.89  119.38    3.51 1.12e+00 7.97e-01 9.84e+00
  angle pdb=" C   LYS A 610 "
        pdb=" CA  LYS A 610 "
        pdb=" CB  LYS A 610 "
      ideal   model   delta    sigma   weight residual
     110.88  115.55   -4.67 1.57e+00 4.06e-01 8.86e+00
  ... (remaining 12709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.70: 5085
       35.70 -    71.39: 409
       71.39 -   107.09: 54
      107.09 -   142.78: 4
      142.78 -   178.48: 5
  Dihedral angle restraints: 5557
    sinusoidal: 3693
      harmonic: 1864
  Sorted by residual:
  dihedral pdb=" O4'   U C  55 "
           pdb=" C1'   U C  55 "
           pdb=" N1    U C  55 "
           pdb=" C2    U C  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.85  155.15     1      1.50e+01 4.44e-03 8.14e+01
  dihedral pdb=" O4'   U C  45 "
           pdb=" C1'   U C  45 "
           pdb=" N1    U C  45 "
           pdb=" C2    U C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   57.13  174.87     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" CA  GLU A  21 "
           pdb=" C   GLU A  21 "
           pdb=" N   ARG A  22 "
           pdb=" CA  ARG A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.04  -19.96     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5554 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1346
       0.046 -    0.093: 128
       0.093 -    0.139: 19
       0.139 -    0.185: 3
       0.185 -    0.232: 2
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CA  PRO A 229 "
            pdb=" N   PRO A 229 "
            pdb=" C   PRO A 229 "
            pdb=" CB  PRO A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C3'   A C 113 "
            pdb=" C4'   A C 113 "
            pdb=" O3'   A C 113 "
            pdb=" C2'   A C 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.54   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C3'   A C  76 "
            pdb=" C4'   A C  76 "
            pdb=" O3'   A C  76 "
            pdb=" C2'   A C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 1495 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 675 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.28e+00
        pdb=" C   ARG A 675 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ARG A 675 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 676 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 427 "   -0.014 2.00e-02 2.50e+03   1.38e-02 3.83e+00
        pdb=" CG  TYR A 427 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 427 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 427 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 427 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 427 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 427 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 427 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 156 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO A 157 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 658
        2.73 -     3.27: 8128
        3.27 -     3.81: 15463
        3.81 -     4.36: 19635
        4.36 -     4.90: 27945
  Nonbonded interactions: 71829
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 714 "
            pdb="ZN    ZN A 801 "
     model   vdw
     2.187 2.230
  nonbonded pdb=" O   ARG A 685 "
            pdb=" OG1 THR A 689 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O2'   U C  13 "
            pdb=" OP2   G C  22 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG1 THR A 466 "
            pdb=" OE1 GLU A 468 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH2 ARG A  26 "
            pdb=" O2'   C C 111 "
     model   vdw
     2.299 3.120
  ... (remaining 71824 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     27.130
  Find NCS groups from input model:        0.070
  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:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
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      :  0.002   0.052   8861  Z= 0.130
  Angle     :  0.526   7.443  12714  Z= 0.329
  Chirality :  0.029   0.232   1498
  Planarity :  0.004   0.041   1088
  Dihedral  : 21.640 178.481   4339
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.01 (0.33), residues: 628
  helix: -0.24 (0.31), residues: 275
  sheet: -3.40 (0.70), residues: 40
  loop : -2.07 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A 159 
 PHE   0.010   0.001   PHE A 398 
 TYR   0.033   0.002   TYR A 427 
 ARG   0.007   0.001   ARG A 638 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8048 (t-100) cc_final: 0.7491 (t-100)
REVERT: A  177 ARG cc_start: 0.8976 (mpt180) cc_final: 0.8533 (mmt180)
REVERT: A  371 ARG cc_start: 0.9227 (tpm170) cc_final: 0.8842 (tpm170)
REVERT: A  631 ASP cc_start: 0.8883 (m-30) cc_final: 0.8400 (p0)
REVERT: A  683 ARG cc_start: 0.9657 (mmp80) cc_final: 0.9224 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.2855
  time to fit residues: 11.9376
Evaluate side-chains
  27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:   30.0000
   chunk 37 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 115 ASN
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 572 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.050103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.040611 restraints weight = 130937.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.041367 restraints weight = 104831.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.041924 restraints weight = 89060.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8861  Z= 0.254
  Angle     :  0.716   7.060  12714  Z= 0.359
  Chirality :  0.039   0.209   1498
  Planarity :  0.005   0.041   1088
  Dihedral  : 23.526 179.265   3081
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 23.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.22 %
    Favored  : 96.58 %
  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: -1.60 (0.32), residues: 628
  helix:  0.06 (0.30), residues: 280
  sheet: -2.87 (0.88), residues: 30
  loop : -1.95 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 724 
 HIS   0.002   0.001   HIS A 440 
 PHE   0.017   0.002   PHE A 756 
 TYR   0.017   0.002   TYR A 427 
 ARG   0.007   0.001   ARG A 754 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8272 (t-100) cc_final: 0.7899 (t-100)
REVERT: A  371 ARG cc_start: 0.9211 (tpm170) cc_final: 0.8816 (tpm170)
REVERT: A  377 TYR cc_start: 0.3093 (m-10) cc_final: 0.2722 (m-10)
REVERT: A  580 MET cc_start: 0.7372 (mtt) cc_final: 0.6921 (mtt)
REVERT: A  631 ASP cc_start: 0.9059 (m-30) cc_final: 0.8585 (p0)
REVERT: A  683 ARG cc_start: 0.9639 (mmp80) cc_final: 0.9333 (mmp80)
  outliers start: 1
  outliers final: 0
  residues processed: 32
  average time/residue: 0.4007
  time to fit residues: 16.9752
Evaluate side-chains
  29 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 60 optimal weight:    0.0270
   chunk 39 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 62 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    6.2046

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A  54 ASN
A 115 ASN
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.046405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.037309 restraints weight = 134005.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.038035 restraints weight = 106620.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.038516 restraints weight = 90129.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8861  Z= 0.260
  Angle     :  0.722   6.509  12714  Z= 0.371
  Chirality :  0.039   0.220   1498
  Planarity :  0.005   0.041   1088
  Dihedral  : 24.098 175.459   3081
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 28.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  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: -1.88 (0.32), residues: 628
  helix:  0.04 (0.30), residues: 280
  sheet: -2.91 (0.84), residues: 29
  loop : -2.35 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 724 
 HIS   0.008   0.002   HIS A 572 
 PHE   0.019   0.003   PHE A 102 
 TYR   0.017   0.002   TYR A 175 
 ARG   0.006   0.001   ARG A  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8357 (t-100) cc_final: 0.8116 (t-100)
REVERT: A  371 ARG cc_start: 0.9402 (tpm170) cc_final: 0.9043 (tpm170)
REVERT: A  377 TYR cc_start: 0.3860 (m-10) cc_final: 0.3521 (m-80)
REVERT: A  631 ASP cc_start: 0.8993 (m-30) cc_final: 0.8373 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.4055
  time to fit residues: 14.3204
Evaluate side-chains
  20 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:   50.0000
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 68 optimal weight:   10.0000
   overall best weight:    5.9188

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.045827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.036217 restraints weight = 134296.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.036997 restraints weight = 106238.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.037564 restraints weight = 88951.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8861  Z= 0.249
  Angle     :  0.723   9.730  12714  Z= 0.368
  Chirality :  0.040   0.270   1498
  Planarity :  0.005   0.054   1088
  Dihedral  : 24.208 176.016   3081
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 28.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.32), residues: 628
  helix:  0.11 (0.31), residues: 278
  sheet: -3.30 (0.80), residues: 30
  loop : -2.45 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  82 
 HIS   0.007   0.002   HIS A 624 
 PHE   0.023   0.002   PHE A 533 
 TYR   0.017   0.002   TYR A 427 
 ARG   0.007   0.001   ARG A 508 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.8324 (t-100) cc_final: 0.8073 (t-100)
REVERT: A  177 ARG cc_start: 0.8968 (mpt180) cc_final: 0.8495 (mmt180)
REVERT: A  377 TYR cc_start: 0.3605 (m-10) cc_final: 0.3073 (m-10)
REVERT: A  628 MET cc_start: -0.1459 (ttt) cc_final: -0.4465 (ttt)
REVERT: A  631 ASP cc_start: 0.8994 (m-30) cc_final: 0.8345 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.3295
  time to fit residues: 10.8556
Evaluate side-chains
  18 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 23 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 55 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 63 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:   11.9994

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  54 ASN
** A 576 HIS ** 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 = 0.3288 r_free = 0.3288 target = 0.040488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.031647 restraints weight = 141385.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.032289 restraints weight = 111377.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.032828 restraints weight = 94412.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.075   8861  Z= 0.469
  Angle     :  1.018  10.346  12714  Z= 0.516
  Chirality :  0.050   0.272   1498
  Planarity :  0.008   0.056   1088
  Dihedral  : 25.058 175.048   3081
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 52.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  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: -2.81 (0.31), residues: 628
  helix: -0.73 (0.29), residues: 274
  sheet: -3.30 (0.66), residues: 44
  loop : -2.75 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A  82 
 HIS   0.007   0.002   HIS A 572 
 PHE   0.031   0.004   PHE A  67 
 TYR   0.027   0.003   TYR A 393 
 ARG   0.008   0.001   ARG A  68 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8727 (t-100) cc_final: 0.8383 (t-100)
REVERT: A  177 ARG cc_start: 0.8388 (mpt180) cc_final: 0.8187 (mmt180)
REVERT: A  631 ASP cc_start: 0.8789 (m-30) cc_final: 0.8167 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.3523
  time to fit residues: 11.4862
Evaluate side-chains
  17 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:   20.0000
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 442 HIS
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 576 HIS ** 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 = 0.3352 r_free = 0.3352 target = 0.042642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.033475 restraints weight = 139388.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.034215 restraints weight = 109958.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.034788 restraints weight = 91755.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.5984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8861  Z= 0.284
  Angle     :  0.802   9.635  12714  Z= 0.413
  Chirality :  0.043   0.277   1498
  Planarity :  0.006   0.075   1088
  Dihedral  : 24.948 174.304   3081
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 37.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  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: -2.53 (0.32), residues: 628
  helix: -0.49 (0.30), residues: 272
  sheet: -3.47 (0.63), residues: 46
  loop : -2.54 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A  82 
 HIS   0.009   0.002   HIS A 681 
 PHE   0.022   0.003   PHE A 733 
 TYR   0.019   0.002   TYR A 393 
 ARG   0.017   0.001   ARG A 683 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8617 (t-100) cc_final: 0.8124 (t-100)
REVERT: A  377 TYR cc_start: 0.5646 (m-80) cc_final: 0.5307 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.3026
  time to fit residues: 10.7167
Evaluate side-chains
  18 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:   40.0000
   chunk 5 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 42 optimal weight:   30.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.042245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.033584 restraints weight = 139422.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.034309 restraints weight = 110604.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.034808 restraints weight = 92786.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.6159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8861  Z= 0.289
  Angle     :  0.799   9.387  12714  Z= 0.411
  Chirality :  0.042   0.279   1498
  Planarity :  0.006   0.058   1088
  Dihedral  : 24.921 174.584   3081
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 38.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  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: -2.47 (0.32), residues: 628
  helix: -0.51 (0.30), residues: 273
  sheet: -3.38 (0.65), residues: 45
  loop : -2.44 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  82 
 HIS   0.005   0.002   HIS A 572 
 PHE   0.018   0.003   PHE A  67 
 TYR   0.018   0.002   TYR A 393 
 ARG   0.019   0.001   ARG A 177 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.8573 (t-100) cc_final: 0.7795 (t-100)
REVERT: A  685 ARG cc_start: 0.8783 (mtt90) cc_final: 0.8569 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3199
  time to fit residues: 9.8851
Evaluate side-chains
  16 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:   50.0000
   chunk 71 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.041991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.033414 restraints weight = 140485.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.034122 restraints weight = 110861.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.034596 restraints weight = 93116.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.6479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8861  Z= 0.290
  Angle     :  0.795   8.946  12714  Z= 0.410
  Chirality :  0.042   0.278   1498
  Planarity :  0.007   0.095   1088
  Dihedral  : 24.964 174.557   3081
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 39.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.61 %
    Favored  : 98.19 %
  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: -2.49 (0.32), residues: 628
  helix: -0.50 (0.31), residues: 272
  sheet: -3.46 (0.65), residues: 45
  loop : -2.46 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  82 
 HIS   0.006   0.002   HIS A 179 
 PHE   0.016   0.003   PHE A 679 
 TYR   0.019   0.002   TYR A 393 
 ARG   0.016   0.001   ARG A 683 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8357 (t-100) cc_final: 0.7770 (t-100)
REVERT: A  377 TYR cc_start: 0.4283 (m-10) cc_final: 0.3974 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2511
  time to fit residues: 8.6023
Evaluate side-chains
  19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:   40.0000
   chunk 54 optimal weight:    0.9980
   chunk 63 optimal weight:   20.0000
   chunk 57 optimal weight:   30.0000
   chunk 24 optimal weight:   30.0000
   chunk 32 optimal weight:    7.9990
   chunk 71 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 0 optimal weight:   40.0000
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.042709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.034045 restraints weight = 138794.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.034782 restraints weight = 108565.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.035275 restraints weight = 90673.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.6542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8861  Z= 0.251
  Angle     :  0.758   8.475  12714  Z= 0.390
  Chirality :  0.041   0.278   1498
  Planarity :  0.006   0.043   1088
  Dihedral  : 24.865 174.307   3081
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 34.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.80 %
    Favored  : 98.99 %
  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: -2.36 (0.32), residues: 628
  helix: -0.44 (0.31), residues: 273
  sheet: -3.47 (0.66), residues: 45
  loop : -2.34 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  82 
 HIS   0.005   0.002   HIS A 681 
 PHE   0.016   0.003   PHE A 533 
 TYR   0.016   0.002   TYR A 393 
 ARG   0.013   0.001   ARG A 683 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8210 (t-100) cc_final: 0.7758 (t-100)
REVERT: A  377 TYR cc_start: 0.4463 (m-10) cc_final: 0.3844 (m-80)
REVERT: A  685 ARG cc_start: 0.8989 (mtt90) cc_final: 0.8616 (mtt180)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2633
  time to fit residues: 8.8311
Evaluate side-chains
  18 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:   50.0000
   chunk 43 optimal weight:   50.0000
   chunk 73 optimal weight:   30.0000
   chunk 19 optimal weight:   20.0000
   chunk 3 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.042261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.033163 restraints weight = 140542.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.033984 restraints weight = 109273.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.034536 restraints weight = 90363.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8861  Z= 0.264
  Angle     :  0.765   7.968  12714  Z= 0.394
  Chirality :  0.041   0.272   1498
  Planarity :  0.006   0.045   1088
  Dihedral  : 24.902 174.584   3081
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 37.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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 (0.32), residues: 628
  helix: -0.48 (0.30), residues: 275
  sheet: -3.55 (0.66), residues: 45
  loop : -2.35 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  82 
 HIS   0.006   0.002   HIS A 179 
 PHE   0.016   0.003   PHE A 533 
 TYR   0.018   0.002   TYR A 393 
 ARG   0.008   0.001   ARG A 698 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8248 (t-100) cc_final: 0.7781 (t-100)
REVERT: A  377 TYR cc_start: 0.4800 (m-10) cc_final: 0.3895 (m-80)
REVERT: A  685 ARG cc_start: 0.8982 (mtt90) cc_final: 0.8687 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2848
  time to fit residues: 8.9401
Evaluate side-chains
  17 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:   30.0000
   chunk 29 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 23 optimal weight:   50.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 563 GLN
** A 576 HIS ** 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 = 0.3375 r_free = 0.3375 target = 0.043382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.034183 restraints weight = 137531.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.034980 restraints weight = 104894.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.035588 restraints weight = 86364.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.6812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8861  Z= 0.218
  Angle     :  0.721   7.557  12714  Z= 0.373
  Chirality :  0.040   0.273   1498
  Planarity :  0.006   0.044   1088
  Dihedral  : 24.728 174.093   3081
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 32.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.80 %
    Favored  : 98.99 %
  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: -2.24 (0.32), residues: 628
  helix: -0.31 (0.30), residues: 275
  sheet: -3.54 (0.66), residues: 45
  loop : -2.29 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  82 
 HIS   0.006   0.002   HIS A 624 
 PHE   0.017   0.002   PHE A 533 
 TYR   0.014   0.002   TYR A 393 
 ARG   0.007   0.001   ARG A 698 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2277.16 seconds
wall clock time: 42 minutes 5.90 seconds (2525.90 seconds total)