Starting phenix.real_space_refine
on Mon Jul 28 00:02:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.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/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2025/7psn_13615.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=  -0.001 sd=   0.089
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
     P      10      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    6088      2.51       5
     N    1604      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9464
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4622
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 17, 'TRANS': 567}
    Chain: "A"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'LOP:plan-2': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 11.07, per 1000 atoms: 1.17
  Number of scatterers: 9464
  At special positions: 0
  Unit cell: (83.628, 75.348, 141.588, 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)
     S      34     16.00
     P      10     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1604      7.00
     C    6088      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: 3.07
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      68.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 93 through 100
    Processing helix  chain 'A' and resid 104 through 140
      removed outlier: 3.747A  pdb=" N   ARG A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 151 through 201
      removed outlier: 3.796A  pdb=" N   ASN A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 210 through 233
    Processing helix  chain 'A' and resid 236 through 253
    Processing helix  chain 'A' and resid 256 through 304
      removed outlier: 3.964A  pdb=" N   TRP A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   HIS A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE A 283 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
    Processing helix  chain 'A' and resid 313 through 367
      removed outlier: 3.583A  pdb=" N   LEU A 317 " --> pdb=" O   ASN A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 396
      Proline residue:  A 388  - end of helix
    Processing helix  chain 'A' and resid 399 through 414
    Processing helix  chain 'A' and resid 475 through 483
      removed outlier: 3.697A  pdb=" N   PHE A 483 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 525 through 531
    Processing helix  chain 'A' and resid 538 through 549
      removed outlier: 3.545A  pdb=" N   VAL A 542 " --> pdb=" O   THR A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 558
    Processing helix  chain 'A' and resid 567 through 571
      removed outlier: 3.514A  pdb=" N   GLY A 570 " --> pdb=" O   GLY A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 590
      removed outlier: 3.738A  pdb=" N   LYS A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
    Processing helix  chain 'A' and resid 632 through 636
      removed outlier: 3.593A  pdb=" N   ILE A 636 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 665 through 676
    Processing helix  chain 'B' and resid 93 through 100
    Processing helix  chain 'B' and resid 104 through 140
      removed outlier: 3.748A  pdb=" N   ARG B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 151 through 201
      removed outlier: 3.796A  pdb=" N   ASN B 185 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 210 through 233
    Processing helix  chain 'B' and resid 236 through 253
    Processing helix  chain 'B' and resid 256 through 304
      removed outlier: 3.964A  pdb=" N   TRP B 279 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   HIS B 282 " --> pdb=" O   ALA B 278 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE B 283 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 310
    Processing helix  chain 'B' and resid 313 through 367
      removed outlier: 3.584A  pdb=" N   LEU B 317 " --> pdb=" O   ASN B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 396
      Proline residue:  B 388  - end of helix
    Processing helix  chain 'B' and resid 399 through 414
    Processing helix  chain 'B' and resid 475 through 483
      removed outlier: 3.696A  pdb=" N   PHE B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 503
      No H-bonds generated for 'chain 'B' and resid 501 through 503'
    Processing helix  chain 'B' and resid 504 through 509
    Processing helix  chain 'B' and resid 525 through 531
    Processing helix  chain 'B' and resid 538 through 549
      removed outlier: 3.545A  pdb=" N   VAL B 542 " --> pdb=" O   THR B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 558
    Processing helix  chain 'B' and resid 567 through 571
      removed outlier: 3.514A  pdb=" N   GLY B 570 " --> pdb=" O   GLY B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 590
      removed outlier: 3.738A  pdb=" N   LYS B 578 " --> pdb=" O   SER B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 617
    Processing helix  chain 'B' and resid 632 through 636
      removed outlier: 3.594A  pdb=" N   ILE B 636 " --> pdb=" O   LEU B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 661
    Processing helix  chain 'B' and resid 665 through 676
    Processing sheet with id=AA1, first strand: chain 'A' and resid 452 through 459
      removed outlier: 5.687A  pdb=" N   LYS A 453 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   PHE A 443 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   PHE A 457 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   GLU A 439 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 437 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   THR A 437 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 441 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   SER A 490 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515
      removed outlier: 6.528A  pdb=" N   MET A 594 " --> pdb=" O   VAL A 627 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ILE A 629 " --> pdb=" O   MET A 594 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A 596 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS A 641 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE A 642 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU A 653 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL A 644 " --> pdb=" O   ARG A 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 459
      removed outlier: 5.687A  pdb=" N   LYS B 453 " --> pdb=" O   PHE B 443 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   PHE B 443 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   PHE B 457 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   GLU B 439 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE B 459 " --> pdb=" O   THR B 437 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   THR B 437 " --> pdb=" O   ILE B 459 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL B 441 " --> pdb=" O   SER B 490 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   SER B 490 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 512 through 515
      removed outlier: 6.529A  pdb=" N   MET B 594 " --> pdb=" O   VAL B 627 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ILE B 629 " --> pdb=" O   MET B 594 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE B 596 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS B 641 " --> pdb=" O   LYS B 464 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B 642 " --> pdb=" O   GLU B 653 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU B 653 " --> pdb=" O   ILE B 642 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B 644 " --> pdb=" O   ARG B 651 " (cutoff:3.500A)

    634 hydrogen bonds defined for protein.
    1878 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: 3.08

  Time building geometry restraints manager: 3.23 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: 1508
        1.31 -     1.43: 2478
        1.43 -     1.56: 5568
        1.56 -     1.68: 14
        1.68 -     1.80: 68
  Bond restraints: 9636
  Sorted by residual:
  bond pdb=" C3' ANP A 701 "
       pdb=" C4' ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.308  0.224 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C3' ANP B 701 "
       pdb=" C4' ANP B 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.308  0.224 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C4' ANP B 701 "
       pdb=" O4' ANP B 701 "
    ideal  model  delta    sigma   weight residual
    1.431  1.626 -0.195 2.00e-02 2.50e+03 9.47e+01
  bond pdb=" C4' ANP A 701 "
       pdb=" O4' ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.431  1.625 -0.194 2.00e-02 2.50e+03 9.45e+01
  bond pdb=" C6  ANP A 701 "
       pdb=" N6  ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.340  1.471 -0.131 2.00e-02 2.50e+03 4.32e+01
  ... (remaining 9631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 12846
        2.77 -     5.54: 126
        5.54 -     8.30: 28
        8.30 -    11.07: 12
       11.07 -    13.84: 8
  Bond angle restraints: 13020
  Sorted by residual:
  angle pdb=" C1' ANP B 701 "
        pdb=" N9  ANP B 701 "
        pdb=" C4  ANP B 701 "
      ideal   model   delta    sigma   weight residual
     125.38  111.54   13.84 3.00e+00 1.11e-01 2.13e+01
  angle pdb=" C1' ANP A 701 "
        pdb=" N9  ANP A 701 "
        pdb=" C4  ANP A 701 "
      ideal   model   delta    sigma   weight residual
     125.38  111.59   13.79 3.00e+00 1.11e-01 2.11e+01
  angle pdb=" O3  LOP A 704 "
        pdb=" P1  LOP A 704 "
        pdb=" O4  LOP A 704 "
      ideal   model   delta    sigma   weight residual
     120.67  109.29   11.38 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" O3  LOP B 704 "
        pdb=" P1  LOP B 704 "
        pdb=" O4  LOP B 704 "
      ideal   model   delta    sigma   weight residual
     120.67  109.32   11.35 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" O3A ANP A 701 "
        pdb=" PA  ANP A 701 "
        pdb=" O5' ANP A 701 "
      ideal   model   delta    sigma   weight residual
      98.09  109.28  -11.19 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 13015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.69: 5505
       25.69 -    51.38: 293
       51.38 -    77.07: 44
       77.07 -   102.76: 8
      102.76 -   128.44: 2
  Dihedral angle restraints: 5852
    sinusoidal: 2468
      harmonic: 3384
  Sorted by residual:
  dihedral pdb=" O1A ANP B 701 "
           pdb=" O3A ANP B 701 "
           pdb=" PA  ANP B 701 "
           pdb=" PB  ANP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -45.33  128.44     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" O1A ANP A 701 "
           pdb=" O3A ANP A 701 "
           pdb=" PA  ANP A 701 "
           pdb=" PB  ANP A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -45.31  128.42     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" O2' ANP B 701 "
           pdb=" C2' ANP B 701 "
           pdb=" C3' ANP B 701 "
           pdb=" O3' ANP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.90  -36.39   84.29     1      3.00e+01 1.11e-03 9.61e+00
  ... (remaining 5849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 954
       0.036 -    0.072: 408
       0.072 -    0.108: 114
       0.108 -    0.144: 14
       0.144 -    0.180: 6
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" C2' ANP A 701 "
            pdb=" C1' ANP A 701 "
            pdb=" C3' ANP A 701 "
            pdb=" O2' ANP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.54   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" C2' ANP B 701 "
            pdb=" C1' ANP B 701 "
            pdb=" C3' ANP B 701 "
            pdb=" O2' ANP B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.55   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" C4  LOP A 704 "
            pdb=" C3  LOP A 704 "
            pdb=" C5  LOP A 704 "
            pdb=" O5  LOP A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34   -2.50    0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 1493 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 LOP B 703 "    0.204 2.00e-02 2.50e+03   2.05e-01 4.21e+02
        pdb=" C14 LOP B 703 "   -0.200 2.00e-02 2.50e+03
        pdb=" C15 LOP B 703 "   -0.210 2.00e-02 2.50e+03
        pdb=" C16 LOP B 703 "    0.206 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 LOP A 703 "   -0.204 2.00e-02 2.50e+03   2.05e-01 4.20e+02
        pdb=" C14 LOP A 703 "    0.200 2.00e-02 2.50e+03
        pdb=" C15 LOP A 703 "    0.210 2.00e-02 2.50e+03
        pdb=" C16 LOP A 703 "   -0.206 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 387 "   -0.005 2.00e-02 2.50e+03   8.91e-03 7.93e-01
        pdb=" C   VAL A 387 "    0.015 2.00e-02 2.50e+03
        pdb=" O   VAL A 387 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PRO A 388 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 70
        2.52 -     3.11: 7626
        3.11 -     3.71: 14350
        3.71 -     4.30: 20897
        4.30 -     4.90: 35778
  Nonbonded interactions: 78721
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 517 "
            pdb="MG    MG B 702 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" OE1 GLN A 517 "
            pdb="MG    MG A 702 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" O2G ANP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O2G ANP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O2B ANP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.047 2.170
  ... (remaining 78716 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.00 max=1.00 mean=0.98
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:             2.690
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.460
  Find NCS groups from input model:        0.170
  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:             0.010
  Load rotamer database and sin/cos tables:14.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
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      :  0.009   0.224   9636  Z= 0.404
  Angle     :  0.823  13.840  13020  Z= 0.365
  Chirality :  0.042   0.180   1496
  Planarity :  0.008   0.205   1620
  Dihedral  : 15.989 128.445   3668
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.21), residues: 1166
  helix: -1.13 (0.16), residues: 772
  sheet: -3.80 (0.43), residues: 52
  loop : -3.49 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 279 
 HIS   0.002   0.001   HIS B 631 
 PHE   0.009   0.001   PHE A 179 
 TYR   0.011   0.002   TYR B 161 
 ARG   0.002   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11032 (  634)
  hydrogen bonds       : angle       5.29664 ( 1878)
  covalent geometry    : bond        0.00903 ( 9636)
  covalent geometry    : angle       0.82288 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 1.3656
  time to fit residues: 178.2282
Evaluate side-chains
  74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 ASN
B 304 ASN
** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.144135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.118305 restraints weight = 10368.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.12
r_work: 0.3325 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9636  Z= 0.135
  Angle     :  0.547   7.487  13020  Z= 0.278
  Chirality :  0.041   0.148   1496
  Planarity :  0.003   0.028   1620
  Dihedral  : 11.709 124.533   1470
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.88 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1166
  helix:  0.68 (0.18), residues: 780
  sheet: -2.66 (0.50), residues: 62
  loop : -2.64 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 279 
 HIS   0.002   0.001   HIS B 197 
 PHE   0.012   0.001   PHE A 391 
 TYR   0.013   0.001   TYR B 161 
 ARG   0.005   0.000   ARG B 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  634)
  hydrogen bonds       : angle       3.81888 ( 1878)
  covalent geometry    : bond        0.00301 ( 9636)
  covalent geometry    : angle       0.54687 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 1.122 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8320 (mm) cc_final: 0.8087 (mp)
REVERT: A  572 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (mmm)
REVERT: A  652 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8378 (mt-10)
REVERT: B  572 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8196 (mmm)
REVERT: B  652 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8370 (mt-10)
  outliers start: 6
  outliers final: 0
  residues processed: 116
  average time/residue: 1.1606
  time to fit residues: 145.1670
Evaluate side-chains
  99 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain B residue  572 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0770
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
A 618 ASN
B 304 ASN
B 618 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.143846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117079 restraints weight = 10453.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.17
r_work: 0.3329 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9636  Z= 0.117
  Angle     :  0.509   7.402  13020  Z= 0.259
  Chirality :  0.040   0.163   1496
  Planarity :  0.003   0.033   1620
  Dihedral  :  9.988 114.104   1470
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.07 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1166
  helix:  1.32 (0.18), residues: 780
  sheet: -2.30 (0.55), residues: 62
  loop : -2.03 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 279 
 HIS   0.003   0.001   HIS B 235 
 PHE   0.013   0.001   PHE B 179 
 TYR   0.011   0.001   TYR B 161 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  634)
  hydrogen bonds       : angle       3.55249 ( 1878)
  covalent geometry    : bond        0.00257 ( 9636)
  covalent geometry    : angle       0.50914 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A  572 MET cc_start: 0.8390 (mmm) cc_final: 0.8176 (mmm)
REVERT: A  652 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8173 (mt-10)
REVERT: B  326 MET cc_start: 0.7343 (mmm) cc_final: 0.7118 (mmm)
REVERT: B  572 MET cc_start: 0.8393 (mmm) cc_final: 0.8185 (mmm)
REVERT: B  652 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8191 (mt-10)
REVERT: B  666 LEU cc_start: 0.6882 (tm) cc_final: 0.6649 (tm)
  outliers start: 9
  outliers final: 0
  residues processed: 117
  average time/residue: 1.0373
  time to fit residues: 132.0210
Evaluate side-chains
  98 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 111 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.141544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.114245 restraints weight = 10606.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.11
r_work: 0.3301 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9636  Z= 0.128
  Angle     :  0.505   6.971  13020  Z= 0.257
  Chirality :  0.040   0.148   1496
  Planarity :  0.003   0.029   1620
  Dihedral  :  9.545 109.877   1470
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.57 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1166
  helix:  1.54 (0.18), residues: 784
  sheet: -2.05 (0.58), residues: 62
  loop : -1.73 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.023   0.001   PHE A 350 
 TYR   0.011   0.001   TYR A 667 
 ARG   0.004   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  634)
  hydrogen bonds       : angle       3.51753 ( 1878)
  covalent geometry    : bond        0.00293 ( 9636)
  covalent geometry    : angle       0.50470 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  556 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7531 (mptt)
REVERT: A  581 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7321 (mp)
REVERT: B  326 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7489 (mmm)
REVERT: B  556 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7536 (mptt)
REVERT: B  581 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7314 (mp)
REVERT: B  652 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8319 (mt-10)
  outliers start: 20
  outliers final: 4
  residues processed: 128
  average time/residue: 1.2559
  time to fit residues: 175.7510
Evaluate side-chains
  108 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 2.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.112967 restraints weight = 10759.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.11
r_work: 0.3267 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9636  Z= 0.138
  Angle     :  0.512   6.825  13020  Z= 0.260
  Chirality :  0.041   0.159   1496
  Planarity :  0.003   0.027   1620
  Dihedral  :  9.303 108.509   1470
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.17 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1166
  helix:  1.66 (0.18), residues: 784
  sheet: -1.86 (0.58), residues: 62
  loop : -1.56 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 279 
 HIS   0.010   0.001   HIS B 235 
 PHE   0.018   0.001   PHE A 350 
 TYR   0.027   0.002   TYR B 161 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  634)
  hydrogen bonds       : angle       3.49242 ( 1878)
  covalent geometry    : bond        0.00322 ( 9636)
  covalent geometry    : angle       0.51170 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 1.143 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7334 (t80) cc_final: 0.6676 (t80)
REVERT: A  556 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7450 (mptt)
REVERT: A  572 MET cc_start: 0.8483 (mmm) cc_final: 0.8117 (tpt)
REVERT: B  326 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7382 (mmm)
REVERT: B  350 PHE cc_start: 0.7342 (t80) cc_final: 0.6684 (t80)
REVERT: B  556 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7465 (mptt)
REVERT: B  572 MET cc_start: 0.8503 (mmm) cc_final: 0.8162 (tpt)
  outliers start: 28
  outliers final: 8
  residues processed: 129
  average time/residue: 1.1749
  time to fit residues: 170.0635
Evaluate side-chains
  108 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.111883 restraints weight = 10852.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.11
r_work: 0.3251 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9636  Z= 0.144
  Angle     :  0.510   6.816  13020  Z= 0.258
  Chirality :  0.041   0.162   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.234 107.151   1470
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.27 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1166
  helix:  1.75 (0.18), residues: 786
  sheet: -2.23 (0.57), residues: 52
  loop : -1.39 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 279 
 HIS   0.012   0.002   HIS B 235 
 PHE   0.017   0.001   PHE B 350 
 TYR   0.026   0.002   TYR B 161 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  634)
  hydrogen bonds       : angle       3.51409 ( 1878)
  covalent geometry    : bond        0.00338 ( 9636)
  covalent geometry    : angle       0.50975 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7311 (t80) cc_final: 0.6654 (t80)
REVERT: A  556 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7427 (mptt)
REVERT: A  572 MET cc_start: 0.8452 (mmm) cc_final: 0.8097 (tpt)
REVERT: A  581 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7138 (mp)
REVERT: A  662 MET cc_start: 0.6678 (tmm) cc_final: 0.6473 (ttt)
REVERT: B  326 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7306 (mmm)
REVERT: B  350 PHE cc_start: 0.7296 (t80) cc_final: 0.6642 (t80)
REVERT: B  556 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7418 (mptt)
REVERT: B  572 MET cc_start: 0.8473 (mmm) cc_final: 0.8125 (tpt)
REVERT: B  581 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7137 (mp)
  outliers start: 24
  outliers final: 10
  residues processed: 123
  average time/residue: 1.0070
  time to fit residues: 134.9795
Evaluate side-chains
  124 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.140119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.113001 restraints weight = 10839.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.13
r_work: 0.3266 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9636  Z= 0.126
  Angle     :  0.494   7.339  13020  Z= 0.251
  Chirality :  0.040   0.155   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.092 105.083   1470
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.67 %
    Favored  : 82.04 %
  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:  1.23 (0.25), residues: 1166
  helix:  1.89 (0.18), residues: 786
  sheet: -2.16 (0.57), residues: 52
  loop : -1.34 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 279 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.014   0.001   PHE A 350 
 TYR   0.031   0.001   TYR B 161 
 ARG   0.003   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  634)
  hydrogen bonds       : angle       3.47053 ( 1878)
  covalent geometry    : bond        0.00286 ( 9636)
  covalent geometry    : angle       0.49372 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7386 (t80) cc_final: 0.6715 (t80)
REVERT: A  556 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7462 (mptt)
REVERT: A  572 MET cc_start: 0.8451 (mmm) cc_final: 0.8107 (tpt)
REVERT: A  662 MET cc_start: 0.6695 (tmm) cc_final: 0.6465 (ttt)
REVERT: B  326 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (mmm)
REVERT: B  350 PHE cc_start: 0.7381 (t80) cc_final: 0.6725 (t80)
REVERT: B  556 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7456 (mptt)
REVERT: B  572 MET cc_start: 0.8470 (mmm) cc_final: 0.8130 (tpt)
  outliers start: 23
  outliers final: 6
  residues processed: 130
  average time/residue: 0.9406
  time to fit residues: 133.5412
Evaluate side-chains
  118 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 112 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.138789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111212 restraints weight = 11027.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.16
r_work: 0.3253 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9636  Z= 0.141
  Angle     :  0.507   7.456  13020  Z= 0.256
  Chirality :  0.040   0.162   1496
  Planarity :  0.003   0.028   1620
  Dihedral  :  9.134 105.643   1470
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.57 %
    Favored  : 81.44 %
  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:  1.30 (0.25), residues: 1166
  helix:  1.93 (0.18), residues: 784
  sheet: -1.69 (0.59), residues: 62
  loop : -1.33 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 463 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.015   0.001   PHE B 350 
 TYR   0.023   0.001   TYR B 161 
 ARG   0.003   0.000   ARG A 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  634)
  hydrogen bonds       : angle       3.51137 ( 1878)
  covalent geometry    : bond        0.00329 ( 9636)
  covalent geometry    : angle       0.50686 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7483 (t80) cc_final: 0.6813 (t80)
REVERT: A  556 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7492 (mptt)
REVERT: A  572 MET cc_start: 0.8526 (mmm) cc_final: 0.8180 (tpt)
REVERT: A  581 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7322 (mp)
REVERT: A  662 MET cc_start: 0.6739 (tmm) cc_final: 0.6469 (ttt)
REVERT: B  326 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7514 (mmm)
REVERT: B  350 PHE cc_start: 0.7408 (t80) cc_final: 0.6791 (t80)
REVERT: B  556 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7496 (mptt)
REVERT: B  572 MET cc_start: 0.8556 (mmm) cc_final: 0.8222 (tpt)
REVERT: B  581 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7284 (mp)
  outliers start: 20
  outliers final: 8
  residues processed: 127
  average time/residue: 1.0347
  time to fit residues: 143.3039
Evaluate side-chains
  121 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0670
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112181 restraints weight = 10880.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.15
r_work: 0.3242 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9636  Z= 0.126
  Angle     :  0.501   7.768  13020  Z= 0.253
  Chirality :  0.040   0.161   1496
  Planarity :  0.003   0.028   1620
  Dihedral  :  9.078 104.588   1470
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.27 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1166
  helix:  2.00 (0.18), residues: 786
  sheet: -2.12 (0.58), residues: 52
  loop : -1.17 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 463 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.014   0.001   PHE B 350 
 TYR   0.017   0.001   TYR B 161 
 ARG   0.004   0.000   ARG B 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  634)
  hydrogen bonds       : angle       3.45802 ( 1878)
  covalent geometry    : bond        0.00289 ( 9636)
  covalent geometry    : angle       0.50101 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7398 (t80) cc_final: 0.6720 (t80)
REVERT: A  556 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7478 (mptt)
REVERT: A  572 MET cc_start: 0.8487 (mmm) cc_final: 0.8149 (tpt)
REVERT: A  581 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7287 (mp)
REVERT: B  134 GLN cc_start: 0.6839 (mt0) cc_final: 0.6599 (mt0)
REVERT: B  326 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7499 (mmm)
REVERT: B  350 PHE cc_start: 0.7372 (t80) cc_final: 0.6668 (t80)
REVERT: B  556 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7482 (mptt)
REVERT: B  572 MET cc_start: 0.8513 (mmm) cc_final: 0.8187 (tpt)
REVERT: B  581 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7282 (mp)
  outliers start: 22
  outliers final: 10
  residues processed: 125
  average time/residue: 1.3505
  time to fit residues: 182.5360
Evaluate side-chains
  119 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0770
   chunk 112 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111607 restraints weight = 10963.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.15
r_work: 0.3238 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9636  Z= 0.129
  Angle     :  0.503   7.895  13020  Z= 0.255
  Chirality :  0.040   0.161   1496
  Planarity :  0.003   0.029   1620
  Dihedral  :  9.064 104.318   1470
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.76 %
    Favored  : 80.44 %
  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:  1.47 (0.25), residues: 1166
  helix:  2.05 (0.18), residues: 784
  sheet: -1.69 (0.59), residues: 62
  loop : -1.19 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 463 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.014   0.001   PHE B 350 
 TYR   0.012   0.001   TYR B 161 
 ARG   0.004   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  634)
  hydrogen bonds       : angle       3.47308 ( 1878)
  covalent geometry    : bond        0.00296 ( 9636)
  covalent geometry    : angle       0.50334 (13020)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  350 PHE cc_start: 0.7274 (t80) cc_final: 0.6559 (t80)
REVERT: A  556 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7401 (mptt)
REVERT: A  572 MET cc_start: 0.8373 (mmm) cc_final: 0.8027 (tpt)
REVERT: B  326 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7315 (mmm)
REVERT: B  350 PHE cc_start: 0.7279 (t80) cc_final: 0.6572 (t80)
REVERT: B  556 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7405 (mptt)
REVERT: B  572 MET cc_start: 0.8414 (mmm) cc_final: 0.8079 (tpt)
REVERT: B  581 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7127 (mp)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.9851
  time to fit residues: 131.0096
Evaluate side-chains
  116 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 107 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111815 restraints weight = 10910.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.15
r_work: 0.3242 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9636  Z= 0.135
  Angle     :  0.512   7.888  13020  Z= 0.259
  Chirality :  0.040   0.164   1496
  Planarity :  0.003   0.028   1620
  Dihedral  :  9.068 104.305   1470
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 18.66 %
    Favored  : 80.04 %
  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:  1.49 (0.25), residues: 1166
  helix:  2.05 (0.18), residues: 784
  sheet: -2.08 (0.58), residues: 52
  loop : -1.11 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 463 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.014   0.001   PHE A 350 
 TYR   0.014   0.001   TYR B 161 
 ARG   0.004   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  634)
  hydrogen bonds       : angle       3.49193 ( 1878)
  covalent geometry    : bond        0.00314 ( 9636)
  covalent geometry    : angle       0.51247 (13020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6291.85 seconds
wall clock time: 112 minutes 7.17 seconds (6727.17 seconds total)