Starting phenix.real_space_refine
on Sat Jan 18 21:18:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vdo_43152/01_2025/8vdo_43152.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.040
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      62      5.16       5
     C    7794      2.51       5
     N    2267      2.21       5
     O    2568      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12691
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1740, 12658
          Classifications: {'peptide': 1740}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 65, 'TRANS': 1674}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
      Conformer: "B"
        Number of residues, atoms: 1740, 12658
          Classifications: {'peptide': 1740}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 65, 'TRANS': 1674}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
          bond proxies already assigned to first conformer: 12754
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A 589 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 589 " occ=0.50
    residue:
      pdb=" N  AARG A 891 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 891 " occ=0.50
    residue:
      pdb=" N  AARG A1136 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A1136 " occ=0.50
  Time building chain proxies: 13.62, per 1000 atoms: 1.07
  Number of scatterers: 12691
  At special positions: 0
  Unit cell: (111.744, 119.808, 148.608, 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      62     16.00
     O    2568      8.00
     N    2267      7.00
     C    7794      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: 3.28
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3266

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 2 sheets defined
      84.9% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 384 through 400
    Processing helix  chain 'A' and resid 489 through 515
      removed outlier: 3.835A  pdb=" N   ASP A 514 " --> pdb=" O   GLN A 510 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP A 515 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 561
    Processing helix  chain 'A' and resid 569 through 600
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 605 through 626
    Processing helix  chain 'A' and resid 633 through 655
      removed outlier: 3.928A  pdb=" N   LEU A 637 " --> pdb=" O   PRO A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 693
    Processing helix  chain 'A' and resid 695 through 724
    Processing helix  chain 'A' and resid 729 through 756
    Processing helix  chain 'A' and resid 759 through 789
      removed outlier: 3.747A  pdb=" N   ALA A 789 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 815
    Processing helix  chain 'A' and resid 818 through 847
    Processing helix  chain 'A' and resid 849 through 880
    Processing helix  chain 'A' and resid 883 through 905
      removed outlier: 3.576A  pdb=" N   GLN A 887 " --> pdb=" O   SER A 883 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 903 " --> pdb=" O   MET A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 941
    Processing helix  chain 'A' and resid 948 through 976
      Proline residue:  A 964  - end of helix
    Processing helix  chain 'A' and resid 979 through 1008
      removed outlier: 4.451A  pdb=" N   GLN A 995 " --> pdb=" O   GLN A 991 " (cutoff:3.500A)
      Proline residue:  A 996  - end of helix
    Processing helix  chain 'A' and resid 1009 through 1011
      No H-bonds generated for 'chain 'A' and resid 1009 through 1011'
    Processing helix  chain 'A' and resid 1013 through 1046
    Processing helix  chain 'A' and resid 1048 through 1073
      removed outlier: 3.771A  pdb=" N   LEU A1054 " --> pdb=" O   MET A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1112
    Processing helix  chain 'A' and resid 1113 through 1142
    Processing helix  chain 'A' and resid 1144 through 1175
      removed outlier: 3.553A  pdb=" N   GLN A1148 " --> pdb=" O   ASP A1144 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   HIS A1175 " --> pdb=" O   LYS A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1202
    Processing helix  chain 'A' and resid 1203 through 1205
      No H-bonds generated for 'chain 'A' and resid 1203 through 1205'
    Processing helix  chain 'A' and resid 1206 through 1225
    Processing helix  chain 'A' and resid 1234 through 1260
    Processing helix  chain 'A' and resid 1263 through 1291
    Processing helix  chain 'A' and resid 1294 through 1325
      removed outlier: 3.889A  pdb=" N   THR A1324 " --> pdb=" O   LYS A1320 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASP A1325 " --> pdb=" O   ALA A1321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1328 through 1353
    Processing helix  chain 'A' and resid 1359 through 1374
      removed outlier: 3.582A  pdb=" N   CYS A1363 " --> pdb=" O   GLY A1359 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR A1372 " --> pdb=" O   ARG A1368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1378
      removed outlier: 3.629A  pdb=" N   GLU A1378 " --> pdb=" O   GLU A1375 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1375 through 1378'
    Processing helix  chain 'A' and resid 1388 through 1417
    Processing helix  chain 'A' and resid 1418 through 1450
    Processing helix  chain 'A' and resid 1463 through 1483
    Processing helix  chain 'A' and resid 1487 through 1516
    Processing helix  chain 'A' and resid 1518 through 1547
    Processing helix  chain 'A' and resid 1551 through 1577
      removed outlier: 3.884A  pdb=" N   ALA A1563 " --> pdb=" O   ARG A1559 " (cutoff:3.500A)
      Proline residue:  A1564  - end of helix
    Processing helix  chain 'A' and resid 1589 through 1623
      Proline residue:  A1598  - end of helix
    Processing helix  chain 'A' and resid 1626 through 1655
      removed outlier: 3.720A  pdb=" N   SER A1631 " --> pdb=" O   PRO A1627 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA A1655 " --> pdb=" O   MET A1651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1657 through 1684
    Processing helix  chain 'A' and resid 1694 through 1722
      removed outlier: 3.555A  pdb=" N   LEU A1698 " --> pdb=" O   SER A1694 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   GLU A1714 " --> pdb=" O   SER A1710 " (cutoff:3.500A)
      Proline residue:  A1715  - end of helix
    Processing helix  chain 'A' and resid 1723 through 1736
      removed outlier: 3.507A  pdb=" N   LEU A1727 " --> pdb=" O   GLU A1723 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   GLY A1728 " --> pdb=" O   ALA A1724 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   HIS A1729 " --> pdb=" O   SER A1725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1737 through 1752
    Processing helix  chain 'A' and resid 1754 through 1783
    Processing helix  chain 'A' and resid 1789 through 1821
      removed outlier: 3.721A  pdb=" N   ALA A1821 " --> pdb=" O   ALA A1817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1826 through 1838
    Processing helix  chain 'A' and resid 1849 through 1878
      removed outlier: 3.924A  pdb=" N   ASN A1876 " --> pdb=" O   VAL A1872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1881 through 1907
      removed outlier: 3.985A  pdb=" N   LYS A1901 " --> pdb=" O   ALA A1897 " (cutoff:3.500A)
      Proline residue:  A1902  - end of helix
    Processing helix  chain 'A' and resid 1909 through 1940
    Processing helix  chain 'A' and resid 1943 through 1972
      removed outlier: 3.520A  pdb=" N   LYS A1947 " --> pdb=" O   ASP A1943 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLY A1971 " --> pdb=" O   ALA A1967 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ASN A1972 " --> pdb=" O   LEU A1968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1972 through 2001
      removed outlier: 4.143A  pdb=" N   ALA A2001 " --> pdb=" O   MET A1997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2014 through 2037
      removed outlier: 4.268A  pdb=" N   GLY A2018 " --> pdb=" O   ASP A2014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2040 through 2070
      removed outlier: 3.562A  pdb=" N   GLY A2070 " --> pdb=" O   ALA A2066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2073 through 2102
      removed outlier: 3.547A  pdb=" N   GLN A2077 " --> pdb=" O   ASP A2073 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A2080 " --> pdb=" O   THR A2076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2108 through 2135
      removed outlier: 4.123A  pdb=" N   TRP A2112 " --> pdb=" O   ASP A2108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 318
      removed outlier: 3.670A  pdb=" N   SER A 311 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   VAL A 337 " --> pdb=" O   GLU A 350 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   GLU A 350 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ARG A 339 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361

    1226 hydrogen bonds defined for protein.
    3672 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: 5.03

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2651
        1.33 -     1.45: 2458
        1.45 -     1.57: 7620
        1.57 -     1.69: 0
        1.69 -     1.81: 97
  Bond restraints: 12826
  Sorted by residual:
  bond pdb=" C   GLU A1463 "
       pdb=" N   PRO A1464 "
    ideal  model  delta    sigma   weight residual
    1.336  1.371 -0.035 1.20e-02 6.94e+03 8.75e+00
  bond pdb=" C   PRO A1464 "
       pdb=" O   PRO A1464 "
    ideal  model  delta    sigma   weight residual
    1.237  1.206  0.031 1.20e-02 6.94e+03 6.68e+00
  bond pdb=" N   THR A1465 "
       pdb=" CA  THR A1465 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.57e+00
  bond pdb=" N   ARG A1469 "
       pdb=" CA  ARG A1469 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.46e+00
  bond pdb=" N   GLN A1466 "
       pdb=" CA  GLN A1466 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.22e+00
  ... (remaining 12821 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 16968
        2.02 -     4.04: 373
        4.04 -     6.06: 49
        6.06 -     8.08: 8
        8.08 -    10.09: 2
  Bond angle restraints: 17400
  Sorted by residual:
  angle pdb=" C   THR A 772 "
        pdb=" CA  THR A 772 "
        pdb=" CB  THR A 772 "
      ideal   model   delta    sigma   weight residual
     110.79  117.82   -7.03 1.66e+00 3.63e-01 1.79e+01
  angle pdb=" CA  LEU A1020 "
        pdb=" C   LEU A1020 "
        pdb=" O   LEU A1020 "
      ideal   model   delta    sigma   weight residual
     120.55  116.77    3.78 1.06e+00 8.90e-01 1.27e+01
  angle pdb=" C   GLN A 783 "
        pdb=" N   HIS A 784 "
        pdb=" CA  HIS A 784 "
      ideal   model   delta    sigma   weight residual
     122.06  115.49    6.57 1.86e+00 2.89e-01 1.25e+01
  angle pdb=" CA  SER A1021 "
        pdb=" C   SER A1021 "
        pdb=" O   SER A1021 "
      ideal   model   delta    sigma   weight residual
     120.55  116.89    3.66 1.06e+00 8.90e-01 1.19e+01
  angle pdb=" CB  MET A1759 "
        pdb=" CG  MET A1759 "
        pdb=" SD  MET A1759 "
      ideal   model   delta    sigma   weight residual
     112.70  102.61   10.09 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 17395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7287
       17.96 -    35.92: 532
       35.92 -    53.88: 102
       53.88 -    71.85: 59
       71.85 -    89.81: 21
  Dihedral angle restraints: 8001
    sinusoidal: 2977
      harmonic: 5024
  Sorted by residual:
  dihedral pdb=" CA  GLU A 599 "
           pdb=" C   GLU A 599 "
           pdb=" N   ASP A 600 "
           pdb=" CA  ASP A 600 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.61   20.39     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  VAL A 380 "
           pdb=" C   VAL A 380 "
           pdb=" N   GLN A 381 "
           pdb=" CA  GLN A 381 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" C   THR A 772 "
           pdb=" N   THR A 772 "
           pdb=" CA  THR A 772 "
           pdb=" CB  THR A 772 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.32    9.32     0      2.50e+00 1.60e-01 1.39e+01
  ... (remaining 7998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1591
       0.043 -    0.086: 406
       0.086 -    0.129: 84
       0.129 -    0.172: 15
       0.172 -    0.215: 6
  Chirality restraints: 2102
  Sorted by residual:
  chirality pdb=" CG  LEU A 609 "
            pdb=" CB  LEU A 609 "
            pdb=" CD1 LEU A 609 "
            pdb=" CD2 LEU A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  VAL A 380 "
            pdb=" CA  VAL A 380 "
            pdb=" CG1 VAL A 380 "
            pdb=" CG2 VAL A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ARG A1035 "
            pdb=" N   ARG A1035 "
            pdb=" C   ARG A1035 "
            pdb=" CB  ARG A1035 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 2099 not shown)

  Planarity restraints: 2313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 772 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.14e+00
        pdb=" C   THR A 772 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   THR A 772 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 773 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 564 "   -0.039 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A 565 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 565 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 565 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1018 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   MET A1018 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET A1018 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A1019 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2310 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1296
        2.74 -     3.28: 13686
        3.28 -     3.82: 23089
        3.82 -     4.36: 25619
        4.36 -     4.90: 44352
  Nonbonded interactions: 108042
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A1250 "
            pdb=" OE1 GLU A1371 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OE2 GLU A1168 "
            pdb=" NH1 ARG A1184 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OD1 ASN A1211 "
            pdb=" NH2 ARG A1214 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   VAL A1640 "
            pdb=" OG  SER A1643 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS A2031 "
            pdb=" NE2 GLN A2035 "
     model   vdw
     2.231 3.120
  ... (remaining 108037 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.220
  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:          0.510
  Check model and map are aligned:         0.110
  Set scattering table:                    0.110
  Process input model:                     39.580
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.090
  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:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  12826  Z= 0.311
  Angle     :  0.718  10.095  17400  Z= 0.425
  Chirality :  0.041   0.215   2102
  Planarity :  0.005   0.059   2313
  Dihedral  : 15.243  89.807   4735
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.30 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.19), residues: 1745
  helix:  1.81 (0.13), residues: 1428
  sheet: -0.22 (0.70), residues: 53
  loop : -1.23 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 351 
 HIS   0.004   0.001   HIS A 784 
 PHE   0.022   0.002   PHE A1390 
 TYR   0.023   0.002   TYR A1893 
 ARG   0.008   0.001   ARG A 889 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.500 
Fit side-chains
REVERT: A  772 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6740 (t)
REVERT: A 1184 ARG cc_start: 0.6547 (mtm110) cc_final: 0.5996 (mtp85)
REVERT: A 1304 ASN cc_start: 0.7159 (m-40) cc_final: 0.6952 (m-40)
REVERT: A 1531 GLU cc_start: 0.7420 (tp30) cc_final: 0.6990 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 154
  average time/residue: 1.3763
  time to fit residues: 231.0379
Evaluate side-chains
  113 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  772 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    0.5980
   chunk 131 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 136 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 101 optimal weight:    0.6980
   chunk 158 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 HIS
A1686 GLN
A1837 GLN
A1854 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.200881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139814 restraints weight = 33087.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 3.29
r_work: 0.3437 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12826  Z= 0.272
  Angle     :  0.607   7.924  17400  Z= 0.321
  Chirality :  0.041   0.211   2102
  Planarity :  0.005   0.054   2313
  Dihedral  :  4.358  29.814   1824
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  7.61 %
    Favored  : 90.44 %
  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:  2.86 (0.19), residues: 1745
  helix:  2.45 (0.13), residues: 1440
  sheet:  0.09 (0.72), residues: 53
  loop : -1.16 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 351 
 HIS   0.015   0.002   HIS A 784 
 PHE   0.019   0.002   PHE A1390 
 TYR   0.022   0.002   TYR A1893 
 ARG   0.006   0.001   ARG A1184 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 1.270 
Fit side-chains
REVERT: A  772 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7219 (t)
REVERT: A 1184 ARG cc_start: 0.6552 (mtm110) cc_final: 0.6267 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.6998 (m-40) cc_final: 0.6779 (m-40)
REVERT: A 1397 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6678 (mtm)
REVERT: A 1455 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7278 (mt0)
REVERT: A 1531 GLU cc_start: 0.7525 (tp30) cc_final: 0.6970 (tp30)
REVERT: A 1910 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6759 (mt-10)
  outliers start: 22
  outliers final: 10
  residues processed: 126
  average time/residue: 1.4125
  time to fit residues: 193.8770
Evaluate side-chains
  124 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue 1333 SER
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1905 VAL
Chi-restraints excluded: chain A residue 2111 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 159 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 155 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 97 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 17 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 HIS
A1686 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.202664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.141549 restraints weight = 36153.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 3.26
r_work: 0.3498 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12826  Z= 0.207
  Angle     :  0.545   8.901  17400  Z= 0.284
  Chirality :  0.038   0.194   2102
  Planarity :  0.004   0.053   2313
  Dihedral  :  4.085  27.438   1824
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  8.58 %
    Favored  : 89.16 %
  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:  3.58 (0.19), residues: 1745
  helix:  2.98 (0.12), residues: 1446
  sheet:  0.00 (0.71), residues: 53
  loop : -1.17 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 351 
 HIS   0.010   0.001   HIS A 784 
 PHE   0.015   0.002   PHE A1390 
 TYR   0.021   0.002   TYR A1893 
 ARG   0.005   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 1.304 
Fit side-chains
REVERT: A  784 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.5906 (p90)
REVERT: A 1153 ASP cc_start: 0.7079 (m-30) cc_final: 0.6742 (m-30)
REVERT: A 1184 ARG cc_start: 0.6573 (mtm110) cc_final: 0.6309 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.7071 (m-40) cc_final: 0.6848 (m-40)
REVERT: A 1397 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6884 (mtm)
REVERT: A 1431 LYS cc_start: 0.8093 (tttt) cc_final: 0.6862 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7529 (mt0)
REVERT: A 1531 GLU cc_start: 0.7448 (tp30) cc_final: 0.6901 (tp30)
REVERT: A 1644 ILE cc_start: 0.7069 (mt) cc_final: 0.6588 (mp)
  outliers start: 26
  outliers final: 10
  residues processed: 136
  average time/residue: 1.3426
  time to fit residues: 199.1195
Evaluate side-chains
  125 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1333 SER
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1573 SER
Chi-restraints excluded: chain A residue 1905 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 153 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 162 optimal weight:   10.0000
   chunk 135 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1686 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.199727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.137873 restraints weight = 27113.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.82
r_work: 0.3461 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12826  Z= 0.332
  Angle     :  0.613   8.473  17400  Z= 0.321
  Chirality :  0.043   0.223   2102
  Planarity :  0.005   0.058   2313
  Dihedral  :  4.207  21.679   1823
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  9.49 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.19 (0.19), residues: 1745
  helix:  2.70 (0.12), residues: 1441
  sheet: -0.01 (0.71), residues: 53
  loop : -1.15 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 351 
 HIS   0.021   0.002   HIS A 784 
 PHE   0.021   0.002   PHE A1390 
 TYR   0.024   0.002   TYR A1893 
 ARG   0.006   0.001   ARG A 898 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7789 (pp30) cc_final: 0.7490 (pp30)
REVERT: A 1184 ARG cc_start: 0.6596 (mtm110) cc_final: 0.6283 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.6991 (m-40) cc_final: 0.6758 (m-40)
REVERT: A 1397 MET cc_start: 0.7113 (mtp) cc_final: 0.6818 (mtm)
REVERT: A 1431 LYS cc_start: 0.8151 (tttt) cc_final: 0.6907 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7618 (mt0)
REVERT: A 1531 GLU cc_start: 0.7619 (tp30) cc_final: 0.7029 (tp30)
REVERT: A 1644 ILE cc_start: 0.7010 (mt) cc_final: 0.6459 (mp)
  outliers start: 30
  outliers final: 20
  residues processed: 132
  average time/residue: 1.3548
  time to fit residues: 195.5853
Evaluate side-chains
  134 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1147 VAL
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1384 ILE
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1571 ASN
Chi-restraints excluded: chain A residue 1573 SER
Chi-restraints excluded: chain A residue 1650 SER
Chi-restraints excluded: chain A residue 1905 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 15 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 160 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.201627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.139524 restraints weight = 35511.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 3.03
r_work: 0.3441 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12826  Z= 0.222
  Angle     :  0.548   8.185  17400  Z= 0.285
  Chirality :  0.038   0.184   2102
  Planarity :  0.004   0.056   2313
  Dihedral  :  4.015  21.094   1823
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.39 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.65 (0.19), residues: 1745
  helix:  3.03 (0.12), residues: 1444
  sheet: -0.06 (0.71), residues: 53
  loop : -1.11 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 351 
 HIS   0.008   0.001   HIS A 784 
 PHE   0.015   0.001   PHE A1390 
 TYR   0.021   0.002   TYR A1893 
 ARG   0.004   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7697 (pp30) cc_final: 0.7421 (pp30)
REVERT: A 1304 ASN cc_start: 0.6878 (m-40) cc_final: 0.6665 (m-40)
REVERT: A 1397 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6706 (mtm)
REVERT: A 1431 LYS cc_start: 0.8091 (tttt) cc_final: 0.6827 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7373 (mt0)
REVERT: A 1531 GLU cc_start: 0.7417 (tp30) cc_final: 0.6832 (tp30)
REVERT: A 1644 ILE cc_start: 0.7045 (mt) cc_final: 0.6513 (mp)
  outliers start: 24
  outliers final: 13
  residues processed: 127
  average time/residue: 1.3642
  time to fit residues: 188.8490
Evaluate side-chains
  128 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1384 ILE
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1571 ASN
Chi-restraints excluded: chain A residue 1573 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 166 optimal weight:    0.8980
   chunk 115 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 157 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 139 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.201408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.139756 restraints weight = 26258.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.82
r_work: 0.3462 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12826  Z= 0.232
  Angle     :  0.547   7.871  17400  Z= 0.284
  Chirality :  0.039   0.183   2102
  Planarity :  0.004   0.056   2313
  Dihedral  :  3.984  20.659   1823
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.77 %
    Favored  : 87.27 %
  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:  3.71 (0.19), residues: 1745
  helix:  3.07 (0.12), residues: 1444
  sheet:  0.01 (0.72), residues: 53
  loop : -1.10 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 351 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.017   0.002   PHE A1390 
 TYR   0.022   0.002   TYR A1893 
 ARG   0.005   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7944 (pp30) cc_final: 0.7662 (pp30)
REVERT: A 1058 GLN cc_start: 0.6850 (mp10) cc_final: 0.6490 (mp-120)
REVERT: A 1304 ASN cc_start: 0.6926 (m-40) cc_final: 0.6715 (m-40)
REVERT: A 1397 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6801 (mtm)
REVERT: A 1431 LYS cc_start: 0.8107 (tttt) cc_final: 0.6837 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7600 (mt0)
REVERT: A 1469 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6342 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7512 (tp30) cc_final: 0.6960 (tp30)
REVERT: A 1644 ILE cc_start: 0.7016 (mt) cc_final: 0.6499 (mp)
  outliers start: 22
  outliers final: 13
  residues processed: 128
  average time/residue: 1.3561
  time to fit residues: 189.9168
Evaluate side-chains
  132 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1469 ARG
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1573 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 154 optimal weight:    0.5980
   chunk 137 optimal weight:    0.5980
   chunk 110 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 153 optimal weight:    0.6980
   chunk 159 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 172 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.202021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.139486 restraints weight = 33211.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.04
r_work: 0.3454 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12826  Z= 0.217
  Angle     :  0.546   8.797  17400  Z= 0.282
  Chirality :  0.038   0.176   2102
  Planarity :  0.004   0.056   2313
  Dihedral  :  3.922  20.135   1823
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.92 %
    Favored  : 86.97 %
  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:  3.84 (0.19), residues: 1745
  helix:  3.16 (0.12), residues: 1445
  sheet:  0.01 (0.72), residues: 53
  loop : -1.05 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 351 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.015   0.001   PHE A1390 
 TYR   0.021   0.002   TYR A1893 
 ARG   0.004   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7584 (tp) cc_final: 0.7319 (mp)
REVERT: A  669 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7829 (tpp)
REVERT: A  670 GLN cc_start: 0.7870 (pp30) cc_final: 0.7540 (pp30)
REVERT: A  703 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6498 (mp)
REVERT: A  995 GLN cc_start: 0.7209 (mp-120) cc_final: 0.6830 (mm-40)
REVERT: A 1304 ASN cc_start: 0.6980 (m-40) cc_final: 0.6776 (m-40)
REVERT: A 1397 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6706 (mtm)
REVERT: A 1431 LYS cc_start: 0.8019 (tttt) cc_final: 0.6779 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7473 (mt0)
REVERT: A 1476 MET cc_start: 0.7272 (mtp) cc_final: 0.7040 (mtp)
REVERT: A 1531 GLU cc_start: 0.7378 (tp30) cc_final: 0.6826 (tp30)
REVERT: A 1644 ILE cc_start: 0.7095 (mt) cc_final: 0.6603 (mp)
REVERT: A 1910 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6684 (mt-10)
  outliers start: 24
  outliers final: 15
  residues processed: 131
  average time/residue: 1.3468
  time to fit residues: 192.4278
Evaluate side-chains
  134 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1573 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 26 optimal weight:    0.0470
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   chunk 145 optimal weight:    0.4980
   chunk 126 optimal weight:    0.3980
   chunk 104 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5880

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.202962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.139099 restraints weight = 39818.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 3.25
r_work: 0.3455 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12826  Z= 0.200
  Angle     :  0.529   7.978  17400  Z= 0.274
  Chirality :  0.037   0.171   2102
  Planarity :  0.004   0.055   2313
  Dihedral  :  3.858  19.690   1823
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.07 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.98 (0.19), residues: 1745
  helix:  3.27 (0.12), residues: 1442
  sheet:  0.09 (0.71), residues: 53
  loop : -1.06 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 351 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.015   0.001   PHE A1390 
 TYR   0.021   0.001   TYR A1893 
 ARG   0.004   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  669 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7918 (tpp)
REVERT: A  670 GLN cc_start: 0.7759 (pp30) cc_final: 0.7420 (pp30)
REVERT: A  703 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6425 (mp)
REVERT: A 1304 ASN cc_start: 0.6855 (m-40) cc_final: 0.6637 (m-40)
REVERT: A 1346 ILE cc_start: 0.6044 (mm) cc_final: 0.5721 (mt)
REVERT: A 1397 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6486 (mtm)
REVERT: A 1431 LYS cc_start: 0.7970 (tttt) cc_final: 0.6728 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7472 (mt0)
REVERT: A 1469 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6193 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7335 (tp30) cc_final: 0.6785 (tp30)
REVERT: A 1606 MET cc_start: 0.5912 (ttp) cc_final: 0.5522 (tmm)
REVERT: A 1644 ILE cc_start: 0.6925 (mt) cc_final: 0.6483 (mp)
REVERT: A 1910 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6716 (mt-10)
  outliers start: 21
  outliers final: 15
  residues processed: 126
  average time/residue: 1.3222
  time to fit residues: 182.3297
Evaluate side-chains
  138 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1058 GLN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1469 ARG
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1573 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 161 optimal weight:    1.9990
   chunk 160 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 158 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 150 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.202520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141156 restraints weight = 30690.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 3.08
r_work: 0.3508 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12826  Z= 0.215
  Angle     :  0.546   8.799  17400  Z= 0.281
  Chirality :  0.038   0.160   2102
  Planarity :  0.004   0.056   2313
  Dihedral  :  3.863  19.539   1823
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.77 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.93 (0.19), residues: 1745
  helix:  3.22 (0.12), residues: 1445
  sheet:  0.12 (0.71), residues: 53
  loop : -1.03 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 351 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.015   0.001   PHE A1390 
 TYR   0.021   0.002   TYR A1893 
 ARG   0.004   0.000   ARG A 827 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7817 (pp30) cc_final: 0.7495 (pp30)
REVERT: A  703 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6473 (mp)
REVERT: A  736 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8189 (tp)
REVERT: A  995 GLN cc_start: 0.7295 (mp-120) cc_final: 0.6890 (mm-40)
REVERT: A 1058 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6360 (mp10)
REVERT: A 1304 ASN cc_start: 0.6950 (m-40) cc_final: 0.6741 (m-40)
REVERT: A 1346 ILE cc_start: 0.6147 (mm) cc_final: 0.5807 (mt)
REVERT: A 1397 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6589 (mtm)
REVERT: A 1431 LYS cc_start: 0.8008 (tttt) cc_final: 0.6774 (tmtt)
REVERT: A 1455 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7627 (mt0)
REVERT: A 1469 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6286 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7431 (tp30) cc_final: 0.6857 (tp30)
REVERT: A 1644 ILE cc_start: 0.7015 (mt) cc_final: 0.6520 (mp)
REVERT: A 1910 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6743 (mt-10)
  outliers start: 27
  outliers final: 17
  residues processed: 131
  average time/residue: 1.4152
  time to fit residues: 202.1208
Evaluate side-chains
  138 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  377 TYR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1058 GLN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1455 GLN
Chi-restraints excluded: chain A residue 1469 ARG
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1573 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 154 optimal weight:    0.0010
   chunk 90 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 26 optimal weight:    0.0570
   overall best weight:    0.3304

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN
** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1455 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.204744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.142929 restraints weight = 36727.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 3.13
r_work: 0.3470 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12826  Z= 0.167
  Angle     :  0.516   9.789  17400  Z= 0.268
  Chirality :  0.036   0.192   2102
  Planarity :  0.004   0.054   2313
  Dihedral  :  3.735  18.425   1823
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.45 %
    Favored  : 86.75 %
  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:  4.25 (0.19), residues: 1745
  helix:  3.46 (0.12), residues: 1443
  sheet:  0.19 (0.72), residues: 51
  loop : -1.01 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1630 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.012   0.001   PHE A1390 
 TYR   0.019   0.001   TYR A1893 
 ARG   0.011   0.000   ARG A 889 

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  703 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6355 (mp)
REVERT: A  995 GLN cc_start: 0.7167 (mp-120) cc_final: 0.6774 (mm-40)
REVERT: A 1304 ASN cc_start: 0.6949 (m-40) cc_final: 0.6735 (m-40)
REVERT: A 1346 ILE cc_start: 0.6046 (mm) cc_final: 0.5723 (mt)
REVERT: A 1397 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6517 (mtm)
REVERT: A 1431 LYS cc_start: 0.7984 (tttt) cc_final: 0.6742 (tmtt)
REVERT: A 1531 GLU cc_start: 0.7311 (tp30) cc_final: 0.6829 (tp30)
REVERT: A 1606 MET cc_start: 0.5991 (ttp) cc_final: 0.5610 (tmm)
REVERT: A 1644 ILE cc_start: 0.7006 (mt) cc_final: 0.6590 (mp)
REVERT: A 1910 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6777 (mt-10)
  outliers start: 20
  outliers final: 14
  residues processed: 133
  average time/residue: 1.3286
  time to fit residues: 193.3520
Evaluate side-chains
  132 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  741 ARG
Chi-restraints excluded: chain A residue  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1058 GLN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1385 ASN
Chi-restraints excluded: chain A residue 1397 MET
Chi-restraints excluded: chain A residue 1449 VAL
Chi-restraints excluded: chain A residue 1520 THR
Chi-restraints excluded: chain A residue 1571 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 155 optimal weight:    0.9990
   chunk 150 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0670
   chunk 133 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1455 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.202920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140884 restraints weight = 34318.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.94
r_work: 0.3457 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12826  Z= 0.213
  Angle     :  0.551   9.451  17400  Z= 0.282
  Chirality :  0.038   0.186   2102
  Planarity :  0.004   0.061   2313
  Dihedral  :  3.814  18.935   1823
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.20 %
    Favored  : 86.07 %
  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:  4.02 (0.19), residues: 1745
  helix:  3.30 (0.12), residues: 1445
  sheet:  0.22 (0.71), residues: 51
  loop : -1.10 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 351 
 HIS   0.011   0.001   HIS A 784 
 PHE   0.016   0.001   PHE A1390 
 TYR   0.021   0.002   TYR A1893 
 ARG   0.013   0.000   ARG A 889 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10535.73 seconds
wall clock time: 186 minutes 45.83 seconds (11205.83 seconds total)