Starting phenix.real_space_refine
on Thu Sep 18 01:09:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vdo_43152/09_2025/8vdo_43152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vdo_43152/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vdo_43152/09_2025/8vdo_43152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vdo_43152/09_2025/8vdo_43152.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vdo_43152/09_2025/8vdo_43152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vdo_43152/09_2025/8vdo_43152.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.040
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.35, per 1000 atoms: 0.50
  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: 1.15
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.43
  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: 2.69

  Time building geometry restraints manager: 1.52 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:             2.350
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.250
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.050
  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:7.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.150
-------------------------------------------------------------------------------
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= 0.228
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG A 889 
 TYR   0.023   0.002   TYR A1893 
 PHE   0.022   0.002   PHE A1390 
 TRP   0.011   0.002   TRP A 351 
 HIS   0.004   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (12826)
  covalent geometry    : angle       0.71807 (17400)
  hydrogen bonds       : bond        0.12064 ( 1226)
  hydrogen bonds       : angle       4.78087 ( 3672)

*********************** 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  : 0.497 
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: 0.6849
  time to fit residues: 114.3421
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  : 0.481 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 665 GLN
** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 HIS
** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1347 ASN
A1369 GLN
A1686 GLN
A1837 GLN
A1854 GLN
A1972 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.199973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136839 restraints weight = 28384.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.72
r_work: 0.3436 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  12826  Z= 0.211
  Angle     :  0.639   8.609  17400  Z= 0.337
  Chirality :  0.043   0.219   2102
  Planarity :  0.005   0.055   2313
  Dihedral  :  4.454  28.871   1824
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  7.38 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.19), residues: 1745
  helix:  2.28 (0.13), residues: 1438
  sheet:  0.00 (0.72), residues: 53
  loop : -1.18 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1184 
 TYR   0.023   0.002   TYR A1893 
 PHE   0.021   0.002   PHE A1390 
 TRP   0.007   0.002   TRP A 359 
 HIS   0.016   0.002   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (12826)
  covalent geometry    : angle       0.63857 (17400)
  hydrogen bonds       : bond        0.05686 ( 1226)
  hydrogen bonds       : angle       3.85055 ( 3672)

*********************** 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
  143 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  772 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7315 (t)
REVERT: A 1184 ARG cc_start: 0.6618 (mtm110) cc_final: 0.6338 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.7085 (m-40) cc_final: 0.6874 (m-40)
REVERT: A 1397 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6744 (mtm)
REVERT: A 1455 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7517 (mt0)
REVERT: A 1531 GLU cc_start: 0.7666 (tp30) cc_final: 0.7045 (tp30)
REVERT: A 1910 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6767 (mt-10)
  outliers start: 29
  outliers final: 14
  residues processed: 128
  average time/residue: 0.6769
  time to fit residues: 94.2987
Evaluate side-chains
  124 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
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  577 VAL
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue 1147 VAL
Chi-restraints excluded: chain A residue 1200 VAL
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 1650 SER
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 119 optimal weight:    3.9990
   chunk 146 optimal weight:    0.9980
   chunk 156 optimal weight:    1.9990
   chunk 148 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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
** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1347 ASN
A1369 GLN
A1686 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.200149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136300 restraints weight = 32992.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.97
r_work: 0.3429 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12826  Z= 0.194
  Angle     :  0.603   8.462  17400  Z= 0.315
  Chirality :  0.042   0.229   2102
  Planarity :  0.005   0.056   2313
  Dihedral  :  4.305  27.387   1824
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  8.89 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.19), residues: 1745
  helix:  2.58 (0.12), residues: 1444
  sheet:  0.03 (0.72), residues: 53
  loop : -1.27 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 898 
 TYR   0.023   0.002   TYR A1893 
 PHE   0.020   0.002   PHE A1390 
 TRP   0.006   0.001   TRP A 351 
 HIS   0.010   0.002   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (12826)
  covalent geometry    : angle       0.60296 (17400)
  hydrogen bonds       : bond        0.05312 ( 1226)
  hydrogen bonds       : angle       3.67054 ( 3672)

*********************** 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
  146 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7763 (pp30) cc_final: 0.7476 (pp30)
REVERT: A  784 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6030 (p90)
REVERT: A 1184 ARG cc_start: 0.6579 (mtm110) cc_final: 0.6291 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.7052 (m-40) cc_final: 0.6835 (m-40)
REVERT: A 1397 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6752 (mtm)
REVERT: A 1455 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7394 (mt0)
REVERT: A 1531 GLU cc_start: 0.7564 (tp30) cc_final: 0.6997 (tp30)
REVERT: A 1644 ILE cc_start: 0.7139 (mt) cc_final: 0.6647 (mp)
REVERT: A 1910 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6800 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 129
  average time/residue: 0.7002
  time to fit residues: 98.0019
Evaluate side-chains
  128 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
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  577 VAL
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 1064 LEU
Chi-restraints excluded: chain A residue 1200 VAL
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 59 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0000
   chunk 148 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0870
   chunk 118 optimal weight:    0.3980
   chunk 46 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.3562

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.203535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.141085 restraints weight = 42014.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.25
r_work: 0.3454 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12826  Z= 0.130
  Angle     :  0.520   6.664  17400  Z= 0.273
  Chirality :  0.037   0.172   2102
  Planarity :  0.004   0.053   2313
  Dihedral  :  3.928  18.023   1823
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.41 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.90 (0.19), residues: 1745
  helix:  3.21 (0.12), residues: 1444
  sheet: -0.01 (0.71), residues: 53
  loop : -1.10 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1184 
 TYR   0.019   0.001   TYR A1893 
 PHE   0.015   0.001   PHE A 664 
 TRP   0.008   0.001   TRP A1630 
 HIS   0.009   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (12826)
  covalent geometry    : angle       0.52005 (17400)
  hydrogen bonds       : bond        0.04399 ( 1226)
  hydrogen bonds       : angle       3.40401 ( 3672)

*********************** 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
  146 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7823 (pp30) cc_final: 0.7582 (pp30)
REVERT: A 1184 ARG cc_start: 0.6367 (mtm110) cc_final: 0.6100 (mtp-110)
REVERT: A 1304 ASN cc_start: 0.6956 (m-40) cc_final: 0.6712 (m-40)
REVERT: A 1397 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6679 (mtm)
REVERT: A 1455 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7379 (mt0)
REVERT: A 1531 GLU cc_start: 0.7342 (tp30) cc_final: 0.6792 (tp30)
REVERT: A 1644 ILE cc_start: 0.7028 (mt) cc_final: 0.6491 (mp)
REVERT: A 1910 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6712 (mt-10)
  outliers start: 22
  outliers final: 10
  residues processed: 136
  average time/residue: 0.7232
  time to fit residues: 106.7465
Evaluate side-chains
  126 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1316 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 1571 ASN
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 81 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 139 optimal weight:    0.6980
   chunk 140 optimal weight:    0.5980
   chunk 8 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.203158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.140621 restraints weight = 34480.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.09
r_work: 0.3504 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    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 = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12826  Z= 0.140
  Angle     :  0.528   8.981  17400  Z= 0.273
  Chirality :  0.037   0.163   2102
  Planarity :  0.004   0.056   2313
  Dihedral  :  3.891  18.802   1823
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.17 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.99 (0.19), residues: 1745
  helix:  3.27 (0.12), residues: 1445
  sheet:  0.02 (0.74), residues: 53
  loop : -1.03 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1184 
 TYR   0.021   0.002   TYR A1893 
 PHE   0.016   0.001   PHE A1390 
 TRP   0.006   0.001   TRP A 351 
 HIS   0.004   0.001   HIS A1501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12826)
  covalent geometry    : angle       0.52772 (17400)
  hydrogen bonds       : bond        0.04437 ( 1226)
  hydrogen bonds       : angle       3.36099 ( 3672)

*********************** 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
  145 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7770 (pp30) cc_final: 0.7507 (pp30)
REVERT: A 1304 ASN cc_start: 0.6959 (m-40) cc_final: 0.6723 (m-40)
REVERT: A 1397 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6579 (mtm)
REVERT: A 1455 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7623 (mt0)
REVERT: A 1531 GLU cc_start: 0.7416 (tp30) cc_final: 0.6847 (tp30)
REVERT: A 1644 ILE cc_start: 0.6957 (mt) cc_final: 0.6452 (mp)
REVERT: A 1910 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6903 (mt-10)
  outliers start: 23
  outliers final: 13
  residues processed: 134
  average time/residue: 0.6609
  time to fit residues: 96.3299
Evaluate side-chains
  131 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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  790 THR
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1316 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 118 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 41 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.201530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.138884 restraints weight = 37259.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 3.43
r_work: 0.3428 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.1434

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= 0.164
  Angle     :  0.547   7.781  17400  Z= 0.286
  Chirality :  0.039   0.193   2102
  Planarity :  0.004   0.057   2313
  Dihedral  :  3.973  19.215   1823
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.77 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.76 (0.19), residues: 1745
  helix:  3.11 (0.12), residues: 1446
  sheet: -0.01 (0.74), residues: 53
  loop : -1.10 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 898 
 TYR   0.022   0.002   TYR A1893 
 PHE   0.017   0.002   PHE A1390 
 TRP   0.005   0.001   TRP A 351 
 HIS   0.008   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12826)
  covalent geometry    : angle       0.54686 (17400)
  hydrogen bonds       : bond        0.04734 ( 1226)
  hydrogen bonds       : angle       3.42316 ( 3672)

*********************** 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
  142 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLN cc_start: 0.7797 (pp30) cc_final: 0.7502 (pp30)
REVERT: A  703 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6515 (mp)
REVERT: A 1058 GLN cc_start: 0.6817 (mt0) cc_final: 0.6291 (mp10)
REVERT: A 1304 ASN cc_start: 0.6790 (m-40) cc_final: 0.6558 (m-40)
REVERT: A 1397 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6445 (mtm)
REVERT: A 1455 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7457 (mt0)
REVERT: A 1531 GLU cc_start: 0.7412 (tp30) cc_final: 0.6890 (tp30)
REVERT: A 1644 ILE cc_start: 0.6945 (mt) cc_final: 0.6426 (mp)
  outliers start: 24
  outliers final: 14
  residues processed: 131
  average time/residue: 0.6565
  time to fit residues: 93.9244
Evaluate side-chains
  134 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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  784 HIS
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1064 LEU
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 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 1775 LEU
Chi-restraints excluded: chain A residue 1905 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 160 optimal weight:    9.9990
   chunk 133 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 173 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 163 optimal weight:    3.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.200784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136615 restraints weight = 27698.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.62
r_work: 0.3491 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12826  Z= 0.187
  Angle     :  0.587   9.413  17400  Z= 0.303
  Chirality :  0.041   0.199   2102
  Planarity :  0.004   0.060   2313
  Dihedral  :  4.054  19.912   1823
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.07 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.54 (0.19), residues: 1745
  helix:  2.94 (0.12), residues: 1444
  sheet:  0.16 (0.74), residues: 53
  loop : -1.15 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 898 
 TYR   0.023   0.002   TYR A1893 
 PHE   0.018   0.002   PHE A1390 
 TRP   0.004   0.001   TRP A 351 
 HIS   0.009   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (12826)
  covalent geometry    : angle       0.58720 (17400)
  hydrogen bonds       : bond        0.05008 ( 1226)
  hydrogen bonds       : angle       3.48771 ( 3672)

*********************** 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
  144 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7017 (pm20)
REVERT: A  670 GLN cc_start: 0.7772 (pp30) cc_final: 0.7501 (pp30)
REVERT: A  703 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6587 (mp)
REVERT: A 1304 ASN cc_start: 0.6917 (m-40) cc_final: 0.6702 (m-40)
REVERT: A 1397 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6791 (mtm)
REVERT: A 1455 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7667 (mt0)
REVERT: A 1469 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6229 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7516 (tp30) cc_final: 0.6930 (tp30)
REVERT: A 1644 ILE cc_start: 0.7081 (mt) cc_final: 0.6552 (mp)
REVERT: A 1910 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6738 (mt-10)
  outliers start: 26
  outliers final: 17
  residues processed: 132
  average time/residue: 0.6822
  time to fit residues: 98.0386
Evaluate side-chains
  136 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
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  567 GLU
Chi-restraints excluded: chain A residue  669 MET
Chi-restraints excluded: chain A residue  703 ILE
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue 1064 LEU
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 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 1571 ASN
Chi-restraints excluded: chain A residue 1573 SER
Chi-restraints excluded: chain A residue 1650 SER
Chi-restraints excluded: chain A residue 1775 LEU
Chi-restraints excluded: chain A residue 1905 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 144 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**

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 = 0.201641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138004 restraints weight = 41082.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 3.41
r_work: 0.3417 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12826  Z= 0.160
  Angle     :  0.551   8.318  17400  Z= 0.287
  Chirality :  0.039   0.182   2102
  Planarity :  0.004   0.058   2313
  Dihedral  :  3.966  19.160   1823
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.14 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.70 (0.19), residues: 1745
  helix:  3.06 (0.12), residues: 1446
  sheet:  0.19 (0.73), residues: 53
  loop : -1.15 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 827 
 TYR   0.022   0.002   TYR A1893 
 PHE   0.016   0.001   PHE A1390 
 TRP   0.005   0.001   TRP A 351 
 HIS   0.008   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (12826)
  covalent geometry    : angle       0.55124 (17400)
  hydrogen bonds       : bond        0.04695 ( 1226)
  hydrogen bonds       : angle       3.41671 ( 3672)

*********************** 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
  141 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6892 (pm20)
REVERT: A  669 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7847 (tpp)
REVERT: A  670 GLN cc_start: 0.7720 (pp30) cc_final: 0.7370 (pp30)
REVERT: A  703 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6542 (mp)
REVERT: A 1304 ASN cc_start: 0.6836 (m-40) cc_final: 0.6616 (m-40)
REVERT: A 1397 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6732 (mtm)
REVERT: A 1455 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7488 (mt0)
REVERT: A 1469 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6213 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7397 (tp30) cc_final: 0.6866 (tp30)
REVERT: A 1644 ILE cc_start: 0.7012 (mt) cc_final: 0.6501 (mp)
REVERT: A 1910 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6693 (mt-10)
  outliers start: 26
  outliers final: 15
  residues processed: 128
  average time/residue: 0.6868
  time to fit residues: 96.0283
Evaluate side-chains
  137 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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  567 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 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 1650 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 173 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   chunk 112 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 115 optimal weight:    7.9990
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 349 GLN
A 374 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.203101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141768 restraints weight = 30322.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 3.15
r_work: 0.3513 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12826  Z= 0.138
  Angle     :  0.537  10.558  17400  Z= 0.276
  Chirality :  0.038   0.174   2102
  Planarity :  0.004   0.058   2313
  Dihedral  :  3.857  18.254   1823
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.52 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.95 (0.19), residues: 1745
  helix:  3.24 (0.12), residues: 1447
  sheet:  0.15 (0.74), residues: 51
  loop : -1.15 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 827 
 TYR   0.021   0.001   TYR A1893 
 PHE   0.014   0.001   PHE A1390 
 TRP   0.006   0.001   TRP A 351 
 HIS   0.008   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12826)
  covalent geometry    : angle       0.53690 (17400)
  hydrogen bonds       : bond        0.04375 ( 1226)
  hydrogen bonds       : angle       3.32470 ( 3672)

*********************** 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
  141 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  567 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6865 (pm20)
REVERT: A  669 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7995 (tpp)
REVERT: A  670 GLN cc_start: 0.7920 (pp30) cc_final: 0.7566 (pp30)
REVERT: A  703 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6506 (mp)
REVERT: A 1058 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6391 (mp10)
REVERT: A 1304 ASN cc_start: 0.6894 (m-40) cc_final: 0.6677 (m-40)
REVERT: A 1397 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6814 (mtm)
REVERT: A 1455 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (mt0)
REVERT: A 1469 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6294 (mtt90)
REVERT: A 1531 GLU cc_start: 0.7431 (tp30) cc_final: 0.6869 (tp30)
REVERT: A 1606 MET cc_start: 0.6082 (ttp) cc_final: 0.5697 (tmm)
REVERT: A 1644 ILE cc_start: 0.7010 (mt) cc_final: 0.6570 (mp)
REVERT: A 1651 MET cc_start: 0.5707 (mmt) cc_final: 0.5431 (mmt)
REVERT: A 1910 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6735 (mt-10)
  outliers start: 25
  outliers final: 14
  residues processed: 126
  average time/residue: 0.6733
  time to fit residues: 92.2053
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  : 0.463 
-------------------------------------------------------------------------------
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  567 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 128 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.202481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.138644 restraints weight = 36988.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 3.15
r_work: 0.3449 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.25   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 = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12826  Z= 0.148
  Angle     :  0.543   8.923  17400  Z= 0.281
  Chirality :  0.038   0.177   2102
  Planarity :  0.004   0.058   2313
  Dihedral  :  3.873  18.420   1823
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.05 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.87 (0.19), residues: 1745
  helix:  3.19 (0.12), residues: 1447
  sheet:  0.10 (0.72), residues: 53
  loop : -1.20 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 827 
 TYR   0.021   0.001   TYR A1893 
 PHE   0.016   0.001   PHE A1390 
 TRP   0.004   0.001   TRP A 351 
 HIS   0.008   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12826)
  covalent geometry    : angle       0.54304 (17400)
  hydrogen bonds       : bond        0.04481 ( 1226)
  hydrogen bonds       : angle       3.34613 ( 3672)

********************** 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
  134 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6826 (pm20)
REVERT: A  669 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7832 (tpp)
REVERT: A  670 GLN cc_start: 0.7822 (pp30) cc_final: 0.7473 (pp30)
REVERT: A  703 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6480 (mp)
REVERT: A 1304 ASN cc_start: 0.6972 (m-40) cc_final: 0.6764 (m-40)
REVERT: A 1397 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6468 (mtm)
REVERT: A 1455 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7387 (mt0)
REVERT: A 1469 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6185 (mtt90)
REVERT: A 1476 MET cc_start: 0.7216 (mtp) cc_final: 0.6911 (mtp)
REVERT: A 1531 GLU cc_start: 0.7365 (tp30) cc_final: 0.6815 (tp30)
REVERT: A 1644 ILE cc_start: 0.6991 (mt) cc_final: 0.6491 (mp)
REVERT: A 1651 MET cc_start: 0.5854 (mmt) cc_final: 0.5336 (mmt)
REVERT: A 1910 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6763 (mt-10)
  outliers start: 20
  outliers final: 14
  residues processed: 123
  average time/residue: 0.6750
  time to fit residues: 90.1984
Evaluate side-chains
  132 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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  567 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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 170 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 160 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 161 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0170
   chunk 99 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 173 optimal weight:    8.9990
   overall best weight:    1.1822

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

Flipped N/Q/H residues before XYZ refinement:
** A2077 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 = 0.4243 r_free = 0.4243 target = 0.200833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.139131 restraints weight = 32221.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 3.05
r_work: 0.3435 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12826  Z= 0.190
  Angle     :  0.602  10.587  17400  Z= 0.310
  Chirality :  0.041   0.202   2102
  Planarity :  0.004   0.060   2313
  Dihedral  :  4.050  19.775   1823
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.97 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.45 (0.19), residues: 1745
  helix:  2.89 (0.12), residues: 1448
  sheet:  0.09 (0.73), residues: 53
  loop : -1.24 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 898 
 TYR   0.023   0.002   TYR A1893 
 PHE   0.019   0.002   PHE A1390 
 TRP   0.004   0.001   TRP A2112 
 HIS   0.010   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12826)
  covalent geometry    : angle       0.60231 (17400)
  hydrogen bonds       : bond        0.05010 ( 1226)
  hydrogen bonds       : angle       3.48601 ( 3672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5845.28 seconds
wall clock time: 100 minutes 27.57 seconds (6027.57 seconds total)