Starting phenix.real_space_refine
on Tue Mar  3 12:16:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2026/6v6c_21068.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2630      2.51       5
     N     667      2.21       5
     O     690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4007
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "L"
      Number of atoms: 4007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4007
          Classifications: {'peptide': 497}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 17, 'TRANS': 479}
          Chain breaks: 12
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 0.85, per 1000 atoms: 0.21
  Number of scatterers: 4007
  At special positions: 0
  Unit cell: (80.1, 77.43, 149.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     690      8.00
     N     667      7.00
     C    2630      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: 0.23
  Conformation dependent library (CDL) restraints added in 148.2 milliseconds
  

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  952

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      69.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'L' and resid 352 through 357
    Processing helix  chain 'L' and resid 392 through 412
      removed outlier: 4.117A  pdb=" N   VAL L 400 " --> pdb=" O   LEU L 396 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TYR L 403 " --> pdb=" O   GLU L 399 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY L 404 " --> pdb=" O   VAL L 400 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   CYS L 406 " --> pdb=" O   GLU L 402 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER L 411 " --> pdb=" O   TYR L 407 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 426 through 447
      removed outlier: 3.534A  pdb=" N   GLN L 430 " --> pdb=" O   GLY L 426 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG L 437 " --> pdb=" O   THR L 433 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG L 438 " --> pdb=" O   SER L 434 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLN L 441 " --> pdb=" O   ARG L 437 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   TYR L 442 " --> pdb=" O   ARG L 438 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 455 through 463
      removed outlier: 3.540A  pdb=" N   ILE L 459 " --> pdb=" O   SER L 455 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY L 460 " --> pdb=" O   LEU L 456 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 463 through 477
      removed outlier: 4.841A  pdb=" N   GLN L 469 " --> pdb=" O   LYS L 465 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ALA L 474 " --> pdb=" O   LEU L 470 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLU L 475 " --> pdb=" O   ARG L 471 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 498 through 512
      removed outlier: 3.893A  pdb=" N   TYR L 506 " --> pdb=" O   LEU L 502 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA L 509 " --> pdb=" O   LEU L 505 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU L 510 " --> pdb=" O   TYR L 506 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASN L 512 " --> pdb=" O   GLU L 508 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 517 through 529
      removed outlier: 3.665A  pdb=" N   LEU L 521 " --> pdb=" O   HIS L 517 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 529 through 540
      removed outlier: 3.752A  pdb=" N   ARG L 534 " --> pdb=" O   GLU L 530 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE L 535 " --> pdb=" O   PRO L 531 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TRP L 539 " --> pdb=" O   PHE L 535 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL L 540 " --> pdb=" O   ILE L 536 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 588 through 606
      removed outlier: 3.615A  pdb=" N   ALA L 592 " --> pdb=" O   LEU L 588 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   HIS L 593 " --> pdb=" O   LYS L 589 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   ASP L 594 " --> pdb=" O   HIS L 590 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR L 596 " --> pdb=" O   ALA L 592 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL L 597 " --> pdb=" O   HIS L 593 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS L 600 " --> pdb=" O   TYR L 596 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE L 602 " --> pdb=" O   CYS L 598 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1477 through 1504
      removed outlier: 4.278A  pdb=" N   THR L1481 " --> pdb=" O   LYS L1477 " (cutoff:3.500A)
      Proline residue:  L1483  - end of helix
      removed outlier: 3.820A  pdb=" N   ALA L1486 " --> pdb=" O   ALA L1482 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   HIS L1487 " --> pdb=" O   PRO L1483 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER L1489 " --> pdb=" O   ALA L1485 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU L1490 " --> pdb=" O   ALA L1486 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE L1499 " --> pdb=" O   ALA L1495 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU L1502 " --> pdb=" O   TYR L1498 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1504 through 1516
      removed outlier: 3.553A  pdb=" N   TYR L1509 " --> pdb=" O   LEU L1505 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLU L1510 " --> pdb=" O   GLU L1506 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   HIS L1514 " --> pdb=" O   GLU L1510 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1523 through 1535
      removed outlier: 4.333A  pdb=" N   ASP L1529 " --> pdb=" O   GLN L1525 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU L1533 " --> pdb=" O   ASP L1529 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LYS L1534 " --> pdb=" O   LEU L1530 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU L1535 " --> pdb=" O   LEU L1531 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1552 through 1558
    Processing helix  chain 'L' and resid 1559 through 1562
      removed outlier: 4.349A  pdb=" N   LEU L1562 " --> pdb=" O   GLN L1559 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1559 through 1562'
    Processing helix  chain 'L' and resid 1601 through 1606
      removed outlier: 3.676A  pdb=" N   ILE L1606 " --> pdb=" O   TRP L1602 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1611 through 1640
      removed outlier: 3.987A  pdb=" N   PHE L1622 " --> pdb=" O   GLY L1618 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   MET L1629 " --> pdb=" O   GLN L1625 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET L1630 " --> pdb=" O   LEU L1626 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LYS L1634 " --> pdb=" O   MET L1630 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1641 through 1644
    Processing helix  chain 'L' and resid 1652 through 1680
      removed outlier: 3.549A  pdb=" N   LEU L1658 " --> pdb=" O   GLN L1654 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   PHE L1661 " --> pdb=" O   GLN L1657 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS L1662 " --> pdb=" O   LEU L1658 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   HIS L1667 " --> pdb=" O   HIS L1663 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE L1668 " --> pdb=" O   GLU L1664 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL L1669 " --> pdb=" O   MET L1665 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY L1674 " --> pdb=" O   LYS L1670 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1682 through 1687
    Processing helix  chain 'L' and resid 1699 through 1715
      removed outlier: 3.718A  pdb=" N   HIS L1710 " --> pdb=" O   ALA L1706 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1722 through 1742
      removed outlier: 3.557A  pdb=" N   MET L1726 " --> pdb=" O   ALA L1722 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE L1729 " --> pdb=" O   VAL L1725 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS L1730 " --> pdb=" O   MET L1726 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   SER L1731 " --> pdb=" O   ASN L1727 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1761 through 1785
      removed outlier: 3.767A  pdb=" N   SER L1768 " --> pdb=" O   LEU L1764 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LYS L1781 " --> pdb=" O   HIS L1777 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR L1784 " --> pdb=" O   PHE L1780 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1793 through 1803
      removed outlier: 4.197A  pdb=" N   ASP L1797 " --> pdb=" O   PRO L1793 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   PHE L1798 " --> pdb=" O   HIS L1794 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU L1799 " --> pdb=" O   LEU L1795 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU L1800 " --> pdb=" O   GLU L1796 " (cutoff:3.500A)

    183 hydrogen bonds defined for protein.
    546 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: 0.49

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1232
        1.35 -     1.46: 1038
        1.46 -     1.58: 1804
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 4102
  Sorted by residual:
  bond pdb=" N   VAL L 353 "
       pdb=" CA  VAL L 353 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.21e-02 6.83e+03 7.81e+00
  bond pdb=" N   LYS L 354 "
       pdb=" CA  LYS L 354 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.35e-02 5.49e+03 4.93e+00
  bond pdb=" N   LEU L 352 "
       pdb=" CA  LEU L 352 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.77e-02 3.19e+03 4.87e+00
  bond pdb=" N   GLU L 351 "
       pdb=" CA  GLU L 351 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.56e+00
  bond pdb=" C   GLU L 351 "
       pdb=" N   LEU L 352 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.013 1.35e-02 5.49e+03 9.67e-01
  ... (remaining 4097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 5453
        1.63 -     3.27: 72
        3.27 -     4.90: 14
        4.90 -     6.54: 4
        6.54 -     8.17: 2
  Bond angle restraints: 5545
  Sorted by residual:
  angle pdb=" O   VAL L 353 "
        pdb=" C   VAL L 353 "
        pdb=" N   LYS L 354 "
      ideal   model   delta    sigma   weight residual
     121.83  124.65   -2.82 1.03e+00 9.43e-01 7.48e+00
  angle pdb=" N   VAL L1783 "
        pdb=" CA  VAL L1783 "
        pdb=" C   VAL L1783 "
      ideal   model   delta    sigma   weight residual
     111.00  108.25    2.75 1.09e+00 8.42e-01 6.37e+00
  angle pdb=" N   LYS L 354 "
        pdb=" CA  LYS L 354 "
        pdb=" C   LYS L 354 "
      ideal   model   delta    sigma   weight residual
     113.01  110.06    2.95 1.20e+00 6.94e-01 6.06e+00
  angle pdb=" CA  VAL L 353 "
        pdb=" C   VAL L 353 "
        pdb=" O   VAL L 353 "
      ideal   model   delta    sigma   weight residual
     120.85  118.34    2.51 1.06e+00 8.90e-01 5.63e+00
  angle pdb=" CA  LEU L 567 "
        pdb=" CB  LEU L 567 "
        pdb=" CG  LEU L 567 "
      ideal   model   delta    sigma   weight residual
     116.30  124.47   -8.17 3.50e+00 8.16e-02 5.45e+00
  ... (remaining 5540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 2122
       16.16 -    32.31: 238
       32.31 -    48.47: 38
       48.47 -    64.63: 5
       64.63 -    80.79: 5
  Dihedral angle restraints: 2408
    sinusoidal: 946
      harmonic: 1462
  Sorted by residual:
  dihedral pdb=" CA  ASP L1601 "
           pdb=" C   ASP L1601 "
           pdb=" N   TRP L1602 "
           pdb=" CA  TRP L1602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.42  -19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  CYS L1686 "
           pdb=" C   CYS L1686 "
           pdb=" N   GLU L1687 "
           pdb=" CA  GLU L1687 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PRO L 451 "
           pdb=" C   PRO L 451 "
           pdb=" N   PRO L 452 "
           pdb=" CA  PRO L 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 2405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 363
       0.030 -    0.060: 207
       0.060 -    0.090: 48
       0.090 -    0.120: 16
       0.120 -    0.151: 1
  Chirality restraints: 635
  Sorted by residual:
  chirality pdb=" CA  VAL L 353 "
            pdb=" N   VAL L 353 "
            pdb=" C   VAL L 353 "
            pdb=" CB  VAL L 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.67e-01
  chirality pdb=" CA  ILE L1608 "
            pdb=" N   ILE L1608 "
            pdb=" C   ILE L1608 "
            pdb=" CB  ILE L1608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CB  VAL L 353 "
            pdb=" CA  VAL L 353 "
            pdb=" CG1 VAL L 353 "
            pdb=" CG2 VAL L 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.52   -0.11 2.00e-01 2.50e+01 2.99e-01
  ... (remaining 632 not shown)

  Planarity restraints: 677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L 351 "    0.011 2.00e-02 2.50e+03   2.39e-02 5.73e+00
        pdb=" C   GLU L 351 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLU L 351 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU L 352 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L1566 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO L1567 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO L1567 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L1567 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN L1546 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO L1547 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO L1547 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO L1547 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 674 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 764
        2.76 -     3.30: 3974
        3.30 -     3.83: 5824
        3.83 -     4.37: 6758
        4.37 -     4.90: 10621
  Nonbonded interactions: 27941
  Sorted by model distance:
  nonbonded pdb=" O   GLY L1611 "
            pdb=" OG  SER L1614 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   PHE L1780 "
            pdb=" OG1 THR L1784 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   PHE L 429 "
            pdb=" OG1 THR L 433 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   MET L1765 "
            pdb=" OG  SER L1768 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA L 445 "
            pdb=" OG  SER L 449 "
     model   vdw
     2.278 3.040
  ... (remaining 27936 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.760
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.000
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
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      :  0.003   0.039   4102  Z= 0.160
  Angle     :  0.547   8.172   5545  Z= 0.297
  Chirality :  0.038   0.151    635
  Planarity :  0.003   0.029    677
  Dihedral  : 13.781  80.787   1456
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.56 (0.32), residues: 471
  helix: -2.93 (0.22), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.89 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 438 
 TYR   0.007   0.001   TYR L 443 
 PHE   0.009   0.001   PHE L 552 
 TRP   0.004   0.001   TRP L1685 
 HIS   0.003   0.001   HIS L1710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4102)
  covalent geometry    : angle       0.54716 ( 5545)
  hydrogen bonds       : bond        0.32763 (  183)
  hydrogen bonds       : angle      10.39023 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: L  464 LYS cc_start: 0.8210 (tppp) cc_final: 0.7704 (ttpt)
REVERT: L  530 GLU cc_start: 0.8772 (tp30) cc_final: 0.8160 (tm-30)
REVERT: L 1493 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8685 (tmmt)
REVERT: L 1638 PHE cc_start: 0.8232 (t80) cc_final: 0.7892 (t80)
REVERT: L 1703 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7817 (mtm180)
REVERT: L 1765 MET cc_start: 0.9222 (mtp) cc_final: 0.8905 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0782
  time to fit residues: 8.3003
Evaluate side-chains
  65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0070
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
L 517 HIS
L1559 GLN
L1702 GLN
** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L1777 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.102438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.092906 restraints weight = 9904.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.094554 restraints weight = 6346.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095725 restraints weight = 4445.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.096504 restraints weight = 3348.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.097090 restraints weight = 2694.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4102  Z= 0.136
  Angle     :  0.566   8.500   5545  Z= 0.290
  Chirality :  0.038   0.126    635
  Planarity :  0.004   0.040    677
  Dihedral  :  4.466  19.074    529
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.38), residues: 471
  helix: -1.18 (0.28), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.60 (0.52), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L1597 
 TYR   0.009   0.001   TYR L 443 
 PHE   0.020   0.001   PHE L1688 
 TRP   0.005   0.001   TRP L 539 
 HIS   0.004   0.001   HIS L1487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4102)
  covalent geometry    : angle       0.56643 ( 5545)
  hydrogen bonds       : bond        0.05618 (  183)
  hydrogen bonds       : angle       5.37444 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: L  530 GLU cc_start: 0.8535 (tp30) cc_final: 0.8126 (tm-30)
REVERT: L  600 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8980 (mtmm)
REVERT: L 1493 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8624 (tmmt)
REVERT: L 1510 GLU cc_start: 0.6794 (pt0) cc_final: 0.6304 (pt0)
REVERT: L 1635 ASP cc_start: 0.8675 (t70) cc_final: 0.8475 (t70)
REVERT: L 1689 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7795 (mmm-85)
REVERT: L 1703 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7801 (mmm-85)
REVERT: L 1765 MET cc_start: 0.9165 (mtp) cc_final: 0.8913 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0743
  time to fit residues: 8.8586
Evaluate side-chains
  71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
L1625 GLN
** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L1759 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.102004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.092893 restraints weight = 9925.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.094565 restraints weight = 6312.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.095753 restraints weight = 4395.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.096623 restraints weight = 3285.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.097235 restraints weight = 2593.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4102  Z= 0.151
  Angle     :  0.577   8.533   5545  Z= 0.291
  Chirality :  0.039   0.119    635
  Planarity :  0.004   0.052    677
  Dihedral  :  4.461  19.486    529
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.39), residues: 471
  helix: -0.56 (0.29), residues: 316
  sheet:  None (None), residues: 0
  loop : -2.55 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 534 
 TYR   0.010   0.001   TYR L 443 
 PHE   0.022   0.002   PHE L1638 
 TRP   0.007   0.001   TRP L 539 
 HIS   0.005   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4102)
  covalent geometry    : angle       0.57713 ( 5545)
  hydrogen bonds       : bond        0.05067 (  183)
  hydrogen bonds       : angle       4.92014 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: L  530 GLU cc_start: 0.8626 (tp30) cc_final: 0.8219 (tm-30)
REVERT: L  600 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8887 (mtmm)
REVERT: L 1489 SER cc_start: 0.8897 (m) cc_final: 0.8627 (p)
REVERT: L 1493 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8690 (tmmt)
REVERT: L 1673 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: L 1703 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7794 (tpp80)
REVERT: L 1795 LEU cc_start: 0.9205 (tp) cc_final: 0.8990 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0581
  time to fit residues: 6.5236
Evaluate side-chains
  69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
L1508 HIS
L1571 ASN
L1705 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.093878 restraints weight = 9776.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095547 restraints weight = 6213.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.096753 restraints weight = 4329.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.097593 restraints weight = 3233.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.098194 restraints weight = 2554.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4102  Z= 0.131
  Angle     :  0.564   8.457   5545  Z= 0.278
  Chirality :  0.038   0.112    635
  Planarity :  0.004   0.041    677
  Dihedral  :  4.338  19.207    529
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.40), residues: 471
  helix: -0.24 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.51 (0.52), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 534 
 TYR   0.008   0.001   TYR L 443 
 PHE   0.020   0.001   PHE L1638 
 TRP   0.006   0.001   TRP L 539 
 HIS   0.005   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4102)
  covalent geometry    : angle       0.56355 ( 5545)
  hydrogen bonds       : bond        0.04519 (  183)
  hydrogen bonds       : angle       4.60017 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7146 (tp30)
REVERT: L  530 GLU cc_start: 0.8636 (tp30) cc_final: 0.8235 (tm-30)
REVERT: L  600 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8880 (mtmm)
REVERT: L 1489 SER cc_start: 0.8976 (m) cc_final: 0.8613 (p)
REVERT: L 1493 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8670 (tmmt)
REVERT: L 1518 MET cc_start: 0.8805 (tpp) cc_final: 0.8270 (tpp)
REVERT: L 1703 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7847 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0668
  time to fit residues: 7.4034
Evaluate side-chains
  65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0870
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.095908 restraints weight = 9869.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.097663 restraints weight = 6145.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098909 restraints weight = 4210.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.099812 restraints weight = 3098.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.100446 restraints weight = 2413.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4102  Z= 0.108
  Angle     :  0.559   8.382   5545  Z= 0.269
  Chirality :  0.036   0.110    635
  Planarity :  0.003   0.042    677
  Dihedral  :  4.181  18.554    529
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.40), residues: 471
  helix:  0.15 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -2.44 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 534 
 TYR   0.011   0.001   TYR L1616 
 PHE   0.012   0.001   PHE L1733 
 TRP   0.006   0.001   TRP L 539 
 HIS   0.004   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4102)
  covalent geometry    : angle       0.55947 ( 5545)
  hydrogen bonds       : bond        0.03920 (  183)
  hydrogen bonds       : angle       4.34131 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7041 (tp30)
REVERT: L  530 GLU cc_start: 0.8632 (tp30) cc_final: 0.8277 (tm-30)
REVERT: L  600 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8821 (mtmm)
REVERT: L 1489 SER cc_start: 0.8913 (m) cc_final: 0.8550 (p)
REVERT: L 1493 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8613 (tmmt)
REVERT: L 1703 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7831 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0611
  time to fit residues: 6.5525
Evaluate side-chains
  65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0570
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.095180 restraints weight = 9890.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.096918 restraints weight = 6159.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.098142 restraints weight = 4262.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.098977 restraints weight = 3167.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.099372 restraints weight = 2515.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4102  Z= 0.116
  Angle     :  0.566   8.263   5545  Z= 0.278
  Chirality :  0.038   0.144    635
  Planarity :  0.003   0.042    677
  Dihedral  :  4.275  18.606    529
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.41), residues: 471
  helix:  0.35 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.38 (0.53), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 534 
 TYR   0.007   0.001   TYR L1498 
 PHE   0.022   0.001   PHE L1499 
 TRP   0.009   0.001   TRP L 539 
 HIS   0.003   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4102)
  covalent geometry    : angle       0.56589 ( 5545)
  hydrogen bonds       : bond        0.04084 (  183)
  hydrogen bonds       : angle       4.30275 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: L  397 LEU cc_start: 0.9392 (tp) cc_final: 0.9178 (tp)
REVERT: L  402 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7036 (tp30)
REVERT: L  530 GLU cc_start: 0.8661 (tp30) cc_final: 0.8280 (tm-30)
REVERT: L  600 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8820 (mtmm)
REVERT: L 1489 SER cc_start: 0.8927 (m) cc_final: 0.8582 (p)
REVERT: L 1493 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8642 (tmmt)
REVERT: L 1518 MET cc_start: 0.8596 (tpp) cc_final: 0.8143 (tpp)
REVERT: L 1703 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7760 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0584
  time to fit residues: 6.1587
Evaluate side-chains
  66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.093118 restraints weight = 10129.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.094820 restraints weight = 6377.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.096001 restraints weight = 4402.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096853 restraints weight = 3279.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.097412 restraints weight = 2589.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4102  Z= 0.140
  Angle     :  0.597   8.254   5545  Z= 0.294
  Chirality :  0.039   0.157    635
  Planarity :  0.003   0.041    677
  Dihedral  :  4.417  19.226    529
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.41), residues: 471
  helix:  0.47 (0.31), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.40 (0.52), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 534 
 TYR   0.014   0.001   TYR L1616 
 PHE   0.011   0.001   PHE L 432 
 TRP   0.008   0.001   TRP L 539 
 HIS   0.005   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4102)
  covalent geometry    : angle       0.59662 ( 5545)
  hydrogen bonds       : bond        0.04342 (  183)
  hydrogen bonds       : angle       4.50967 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7607 (mm-30) cc_final: 0.6954 (tp30)
REVERT: L  530 GLU cc_start: 0.8725 (tp30) cc_final: 0.8332 (tm-30)
REVERT: L  600 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8828 (mtmm)
REVERT: L 1489 SER cc_start: 0.8944 (m) cc_final: 0.8593 (p)
REVERT: L 1493 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8706 (tmmt)
REVERT: L 1703 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7678 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0707
  time to fit residues: 6.9389
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.095037 restraints weight = 9896.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096908 restraints weight = 6075.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.098087 restraints weight = 4141.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.098974 restraints weight = 3084.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.099660 restraints weight = 2404.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4102  Z= 0.110
  Angle     :  0.585   9.195   5545  Z= 0.281
  Chirality :  0.038   0.138    635
  Planarity :  0.003   0.042    677
  Dihedral  :  4.292  19.768    529
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.41), residues: 471
  helix:  0.63 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.27 (0.53), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 534 
 TYR   0.009   0.001   TYR L1675 
 PHE   0.010   0.001   PHE L1733 
 TRP   0.008   0.001   TRP L 539 
 HIS   0.003   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4102)
  covalent geometry    : angle       0.58525 ( 5545)
  hydrogen bonds       : bond        0.03912 (  183)
  hydrogen bonds       : angle       4.28747 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6918 (tp30)
REVERT: L  530 GLU cc_start: 0.8727 (tp30) cc_final: 0.8299 (tm-30)
REVERT: L  532 TYR cc_start: 0.8684 (t80) cc_final: 0.7878 (t80)
REVERT: L  600 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8823 (mtmm)
REVERT: L 1489 SER cc_start: 0.8966 (m) cc_final: 0.8605 (p)
REVERT: L 1493 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8644 (tmmt)
REVERT: L 1528 SER cc_start: 0.9468 (p) cc_final: 0.9245 (p)
REVERT: L 1689 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7689 (mmm-85)
REVERT: L 1703 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7625 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0683
  time to fit residues: 7.1762
Evaluate side-chains
  66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 24 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0370
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.3460

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.096187 restraints weight = 9980.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.098042 restraints weight = 6163.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.099296 restraints weight = 4191.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.100190 restraints weight = 3074.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.100693 restraints weight = 2397.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4102  Z= 0.102
  Angle     :  0.570   8.093   5545  Z= 0.276
  Chirality :  0.038   0.132    635
  Planarity :  0.003   0.043    677
  Dihedral  :  4.181  20.029    529
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.41), residues: 471
  helix:  0.68 (0.30), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.08 (0.55), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 534 
 TYR   0.009   0.001   TYR L1675 
 PHE   0.013   0.001   PHE L1733 
 TRP   0.007   0.001   TRP L 539 
 HIS   0.002   0.000   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 4102)
  covalent geometry    : angle       0.57016 ( 5545)
  hydrogen bonds       : bond        0.03678 (  183)
  hydrogen bonds       : angle       4.21957 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6946 (tp30)
REVERT: L  430 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: L  502 LEU cc_start: 0.9025 (tp) cc_final: 0.8503 (tp)
REVERT: L  530 GLU cc_start: 0.8683 (tp30) cc_final: 0.8332 (tm-30)
REVERT: L  532 TYR cc_start: 0.8676 (t80) cc_final: 0.7864 (t80)
REVERT: L  600 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8825 (mtmm)
REVERT: L 1489 SER cc_start: 0.8962 (m) cc_final: 0.8596 (p)
REVERT: L 1493 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8615 (tmmt)
REVERT: L 1639 HIS cc_start: 0.8385 (t70) cc_final: 0.7816 (t-170)
REVERT: L 1689 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7677 (mmm-85)
REVERT: L 1703 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7638 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0620
  time to fit residues: 6.7261
Evaluate side-chains
  68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0040
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0470
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3890

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.106218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.096971 restraints weight = 9914.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098751 restraints weight = 6195.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.099964 restraints weight = 4270.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.100802 restraints weight = 3160.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.101206 restraints weight = 2486.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4102  Z= 0.106
  Angle     :  0.586   8.040   5545  Z= 0.284
  Chirality :  0.039   0.150    635
  Planarity :  0.003   0.042    677
  Dihedral  :  4.197  19.339    529
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.41), residues: 471
  helix:  0.68 (0.30), residues: 316
  sheet:  None (None), residues: 0
  loop : -1.96 (0.55), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 534 
 TYR   0.009   0.001   TYR L1675 
 PHE   0.006   0.001   PHE L 432 
 TRP   0.007   0.001   TRP L 539 
 HIS   0.001   0.000   HIS L 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4102)
  covalent geometry    : angle       0.58606 ( 5545)
  hydrogen bonds       : bond        0.03641 (  183)
  hydrogen bonds       : angle       4.23585 (  546)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: L  402 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6975 (tp30)
REVERT: L  430 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8503 (tm-30)
REVERT: L  502 LEU cc_start: 0.9050 (tp) cc_final: 0.8555 (tp)
REVERT: L  530 GLU cc_start: 0.8654 (tp30) cc_final: 0.8332 (tm-30)
REVERT: L  532 TYR cc_start: 0.8641 (t80) cc_final: 0.7880 (t80)
REVERT: L  600 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8814 (mtmm)
REVERT: L 1489 SER cc_start: 0.8975 (m) cc_final: 0.8622 (p)
REVERT: L 1493 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8634 (tmmt)
REVERT: L 1639 HIS cc_start: 0.8329 (t70) cc_final: 0.7793 (t-170)
REVERT: L 1689 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7610 (mmm-85)
REVERT: L 1703 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7636 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0641
  time to fit residues: 6.7835
Evaluate side-chains
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0770
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5416

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

Flipped N/Q/H residues before XYZ refinement:
L1571 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.104853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.095696 restraints weight = 9926.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.097483 restraints weight = 6133.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098659 restraints weight = 4191.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.099530 restraints weight = 3103.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.100112 restraints weight = 2424.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4102  Z= 0.116
  Angle     :  0.589   7.930   5545  Z= 0.287
  Chirality :  0.039   0.129    635
  Planarity :  0.003   0.042    677
  Dihedral  :  4.232  19.464    529
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.41), residues: 471
  helix:  0.75 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.09 (0.54), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 534 
 TYR   0.008   0.001   TYR L1675 
 PHE   0.014   0.001   PHE L1688 
 TRP   0.009   0.001   TRP L 539 
 HIS   0.002   0.001   HIS L1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4102)
  covalent geometry    : angle       0.58912 ( 5545)
  hydrogen bonds       : bond        0.03839 (  183)
  hydrogen bonds       : angle       4.29546 (  546)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 812.41 seconds
wall clock time: 14 minutes 36.19 seconds (876.19 seconds total)