Starting phenix.real_space_refine
on Tue Feb 11 23:13:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xe6_22144/02_2025/6xe6_22144.cif"
  }
  resolution = 4.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      54      5.16       5
     C    4298      2.51       5
     N    1022      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6530
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 826, 6340
          Classifications: {'peptide': 826}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 36, 'TRANS': 789}
          Chain breaks: 10
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 335
          Unresolved non-hydrogen dihedrals: 232
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 190
          Unusual residues: {'NAG': 1, 'Y01': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 4.69, per 1000 atoms: 0.72
  Number of scatterers: 6530
  At special positions: 0
  Unit cell: (99.96, 74.97, 119.119, 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      54     16.00
     O    1156      8.00
     N    1022      7.00
     C    4298      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 367 " distance=2.04

  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: 1.65
  Conformation dependent library (CDL) restraints added in 926.3 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      62.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 188
      removed outlier: 3.547A  pdb=" N   TRP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 210
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.534A  pdb=" N   ASN A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 4.701A  pdb=" N   CYS A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 432
      removed outlier: 3.974A  pdb=" N   ILE A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 472
    Processing helix  chain 'A' and resid 491 through 523
      removed outlier: 4.545A  pdb=" N   GLN A 497 " --> pdb=" O   HIS A 493 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   LEU A 501 " --> pdb=" O   GLN A 497 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   MET A 502 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR A 506 " --> pdb=" O   MET A 502 " (cutoff:3.500A)
      Proline residue:  A 507  - end of helix
      removed outlier: 3.527A  pdb=" N   LYS A 523 " --> pdb=" O   CYS A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 549
      removed outlier: 3.562A  pdb=" N   THR A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 549 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 570
      removed outlier: 3.792A  pdb=" N   THR A 561 " --> pdb=" O   PHE A 557 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU A 563 " --> pdb=" O   ASN A 559 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 588
      removed outlier: 3.713A  pdb=" N   PHE A 575 " --> pdb=" O   ALA A 571 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 576 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASP A 579 " --> pdb=" O   PHE A 575 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 586 " --> pdb=" O   ASN A 582 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A 587 " --> pdb=" O   TYR A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 623
      removed outlier: 3.617A  pdb=" N   THR A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA A 618 " --> pdb=" O   THR A 614 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   PHE A 619 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 661
      removed outlier: 3.827A  pdb=" N   ARG A 631 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL A 646 " --> pdb=" O   LEU A 642 " (cutoff:3.500A)
      Proline residue:  A 653  - end of helix
    Processing helix  chain 'A' and resid 689 through 716
      Proline residue:  A 711  - end of helix
    Processing helix  chain 'A' and resid 719 through 736
      removed outlier: 3.874A  pdb=" N   PHE A 723 " --> pdb=" O   TYR A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.659A  pdb=" N   ARG A 763 " --> pdb=" O   HIS A 759 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ASP A 765 " --> pdb=" O   PHE A 761 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A 766 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 837
    Processing helix  chain 'A' and resid 852 through 862
      removed outlier: 3.613A  pdb=" N   PHE A 856 " --> pdb=" O   PHE A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 896
    Processing helix  chain 'A' and resid 938 through 955
      removed outlier: 3.558A  pdb=" N   GLN A 942 " --> pdb=" O   GLU A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 1003
      removed outlier: 3.507A  pdb=" N   ASP A 975 " --> pdb=" O   LEU A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1030
      removed outlier: 3.569A  pdb=" N   GLY A1025 " --> pdb=" O   PHE A1021 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL A1028 " --> pdb=" O   VAL A1024 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A1030 " --> pdb=" O   SER A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1062
      removed outlier: 3.987A  pdb=" N   HIS A1055 " --> pdb=" O   ASP A1051 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A1059 " --> pdb=" O   HIS A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1096
      removed outlier: 4.625A  pdb=" N   MET A1085 " --> pdb=" O   SER A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1134
      removed outlier: 3.690A  pdb=" N   THR A1106 " --> pdb=" O   VAL A1102 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA A1121 " --> pdb=" O   CYS A1117 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   CYS A1133 " --> pdb=" O   CYS A1129 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    1071 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: 1.66

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1050
        1.33 -     1.45: 1802
        1.45 -     1.57: 3758
        1.57 -     1.70: 3
        1.70 -     1.82: 85
  Bond restraints: 6698
  Sorted by residual:
  bond pdb=" CAX Y01 A1303 "
       pdb=" OAH Y01 A1303 "
    ideal  model  delta    sigma   weight residual
    1.248  1.345 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" CAX Y01 A1304 "
       pdb=" OAH Y01 A1304 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" CAX Y01 A1302 "
       pdb=" OAH Y01 A1302 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" CAX Y01 A1305 "
       pdb=" OAH Y01 A1305 "
    ideal  model  delta    sigma   weight residual
    1.248  1.344 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" CAX Y01 A1301 "
       pdb=" OAH Y01 A1301 "
    ideal  model  delta    sigma   weight residual
    1.248  1.343 -0.095 2.00e-02 2.50e+03 2.25e+01
  ... (remaining 6693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8057
        2.13 -     4.26: 989
        4.26 -     6.39: 74
        6.39 -     8.52: 14
        8.52 -    10.65: 4
  Bond angle restraints: 9138
  Sorted by residual:
  angle pdb=" C   HIS A 759 "
        pdb=" N   PRO A 760 "
        pdb=" CA  PRO A 760 "
      ideal   model   delta    sigma   weight residual
     119.84  130.49  -10.65 1.25e+00 6.40e-01 7.26e+01
  angle pdb=" N   PRO A 439 "
        pdb=" CA  PRO A 439 "
        pdb=" CB  PRO A 439 "
      ideal   model   delta    sigma   weight residual
     103.25  111.16   -7.91 1.05e+00 9.07e-01 5.67e+01
  angle pdb=" N   PRO A 447 "
        pdb=" CA  PRO A 447 "
        pdb=" CB  PRO A 447 "
      ideal   model   delta    sigma   weight residual
     103.00  110.09   -7.09 1.10e+00 8.26e-01 4.16e+01
  angle pdb=" N   PRO A 415 "
        pdb=" CA  PRO A 415 "
        pdb=" CB  PRO A 415 "
      ideal   model   delta    sigma   weight residual
     103.00  109.71   -6.71 1.10e+00 8.26e-01 3.72e+01
  angle pdb=" N   TYR A 300 "
        pdb=" CA  TYR A 300 "
        pdb=" C   TYR A 300 "
      ideal   model   delta    sigma   weight residual
     111.03  117.61   -6.58 1.11e+00 8.12e-01 3.52e+01
  ... (remaining 9133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3725
       17.13 -    34.26: 331
       34.26 -    51.40: 102
       51.40 -    68.53: 16
       68.53 -    85.66: 2
  Dihedral angle restraints: 4176
    sinusoidal: 1753
      harmonic: 2423
  Sorted by residual:
  dihedral pdb=" CA  LYS A 588 "
           pdb=" C   LYS A 588 "
           pdb=" N   PRO A 589 "
           pdb=" CA  PRO A 589 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.51  -29.49     0      5.00e+00 4.00e-02 3.48e+01
  dihedral pdb=" CB  CYS A 323 "
           pdb=" SG  CYS A 323 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.42   47.58     1      1.00e+01 1.00e-02 3.12e+01
  dihedral pdb=" CA  ALA A1082 "
           pdb=" C   ALA A1082 "
           pdb=" N   MET A1083 "
           pdb=" CA  MET A1083 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.97  -26.03     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 4173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 852
       0.078 -    0.157: 179
       0.157 -    0.235: 33
       0.235 -    0.313: 7
       0.313 -    0.392: 5
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" CBG Y01 A1303 "
            pdb=" CAQ Y01 A1303 "
            pdb=" CBD Y01 A1303 "
            pdb=" CBI Y01 A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.72    0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CBG Y01 A1305 "
            pdb=" CAQ Y01 A1305 "
            pdb=" CBD Y01 A1305 "
            pdb=" CBI Y01 A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CBG Y01 A1304 "
            pdb=" CAQ Y01 A1304 "
            pdb=" CBD Y01 A1304 "
            pdb=" CBI Y01 A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.37 2.00e-01 2.50e+01 3.49e+00
  ... (remaining 1073 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 879 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO A 880 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 880 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 880 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 876 "    0.022 2.00e-02 2.50e+03   1.94e-02 5.64e+00
        pdb=" CG  HIS A 876 "   -0.037 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 876 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 876 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 876 "    0.017 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 876 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 316 "    0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO A 317 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        1.10 -     1.86: 3
        1.86 -     2.62: 42
        2.62 -     3.38: 9038
        3.38 -     4.14: 14438
        4.14 -     4.90: 24894
  Nonbonded interactions: 48415
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 836 "
            pdb=" O1  NAG A1306 "
     model   vdw
     1.098 3.040
  nonbonded pdb=" O   SER A 820 "
            pdb=" NE2 GLN A 883 "
     model   vdw
     1.733 3.120
  nonbonded pdb=" O   PRO A 910 "
            pdb=" O   ALA A 922 "
     model   vdw
     1.773 3.040
  nonbonded pdb=" CG  ASN A 836 "
            pdb=" O1  NAG A1306 "
     model   vdw
     2.181 3.270
  nonbonded pdb=" O   VAL A 610 "
            pdb=" OG1 THR A 614 "
     model   vdw
     2.266 3.040
  ... (remaining 48410 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.990
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
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      :  0.011   0.139   6698  Z= 0.688
  Angle     :  1.399  10.649   9138  Z= 0.913
  Chirality :  0.072   0.392   1076
  Planarity :  0.005   0.065   1104
  Dihedral  : 14.626  85.659   2597
  Min Nonbonded Distance : 1.098

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  : 11.32 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.38 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.98 (0.22), residues: 804
  helix: -2.36 (0.18), residues: 473
  sheet:  None (None), residues: 0
  loop : -4.80 (0.25), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 826 
 HIS   0.017   0.002   HIS A 876 
 PHE   0.024   0.003   PHE A 839 
 TYR   0.019   0.002   TYR A 764 
 ARG   0.010   0.001   ARG A1078 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 232
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  220 LEU cc_start: 0.9012 (pp) cc_final: 0.8792 (pp)
REVERT: A  221 LEU cc_start: 0.9445 (tp) cc_final: 0.9056 (tp)
REVERT: A  383 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6452 (tpt-90)
REVERT: A  433 ASP cc_start: 0.7709 (m-30) cc_final: 0.7436 (m-30)
REVERT: A  453 MET cc_start: 0.5448 (pmm) cc_final: 0.4694 (pmm)
REVERT: A  465 MET cc_start: 0.8420 (ttt) cc_final: 0.7961 (tpt)
REVERT: A  573 ASP cc_start: 0.8357 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  578 CYS cc_start: 0.8937 (m) cc_final: 0.8595 (m)
REVERT: A  581 TRP cc_start: 0.8950 (t-100) cc_final: 0.8185 (t-100)
REVERT: A  597 VAL cc_start: 0.9693 (p) cc_final: 0.9402 (p)
REVERT: A  620 TYR cc_start: 0.8790 (m-80) cc_final: 0.8158 (m-80)
REVERT: A  796 GLU cc_start: 0.8965 (tt0) cc_final: 0.8686 (tt0)
REVERT: A  798 ASN cc_start: 0.7981 (p0) cc_final: 0.7290 (t0)
REVERT: A  889 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8387 (m)
REVERT: A  970 ASN cc_start: 0.8277 (p0) cc_final: 0.8018 (p0)
REVERT: A 1011 TYR cc_start: 0.8822 (m-10) cc_final: 0.6857 (m-80)
REVERT: A 1029 LEU cc_start: 0.9265 (tp) cc_final: 0.9003 (tp)
REVERT: A 1032 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6775 (t60)
REVERT: A 1034 LEU cc_start: 0.9423 (tt) cc_final: 0.8887 (mp)
REVERT: A 1052 PHE cc_start: 0.8249 (m-80) cc_final: 0.8013 (m-80)
REVERT: A 1083 MET cc_start: 0.8866 (mmp) cc_final: 0.8645 (mmm)
REVERT: A 1101 THR cc_start: 0.9146 (m) cc_final: 0.8946 (m)
REVERT: A 1112 MET cc_start: 0.8317 (ppp) cc_final: 0.7541 (ppp)
  outliers start: 7
  outliers final: 2
  residues processed: 236
  average time/residue: 0.1540
  time to fit residues: 50.1251
Evaluate side-chains
  189 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 185
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 559 ASN
A 778 HIS
A 941 HIS
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.109265 restraints weight = 14195.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112655 restraints weight = 8905.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115049 restraints weight = 6147.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   6698  Z= 0.329
  Angle     :  0.823   8.901   9138  Z= 0.427
  Chirality :  0.048   0.228   1076
  Planarity :  0.005   0.038   1104
  Dihedral  :  8.968  56.568   1248
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.70 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  4.66 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.27), residues: 804
  helix: -0.66 (0.22), residues: 491
  sheet:  None (None), residues: 0
  loop : -4.38 (0.28), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 826 
 HIS   0.006   0.001   HIS A 429 
 PHE   0.032   0.003   PHE A 725 
 TYR   0.036   0.002   TYR A1011 
 ARG   0.004   0.001   ARG A1132 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9386 (tp) cc_final: 0.9000 (tp)
REVERT: A  302 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.7024 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7807 (mtt180) cc_final: 0.6561 (tpt-90)
REVERT: A  453 MET cc_start: 0.5459 (pmm) cc_final: 0.5174 (pmm)
REVERT: A  465 MET cc_start: 0.8428 (ttt) cc_final: 0.7979 (tpp)
REVERT: A  489 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7044 (p90)
REVERT: A  540 ILE cc_start: 0.9307 (pt) cc_final: 0.9079 (tp)
REVERT: A  573 ASP cc_start: 0.8794 (m-30) cc_final: 0.8383 (m-30)
REVERT: A  578 CYS cc_start: 0.9430 (m) cc_final: 0.9089 (m)
REVERT: A  581 TRP cc_start: 0.8964 (t-100) cc_final: 0.7996 (t-100)
REVERT: A  596 THR cc_start: 0.9357 (p) cc_final: 0.9153 (p)
REVERT: A  597 VAL cc_start: 0.9739 (p) cc_final: 0.9392 (p)
REVERT: A  636 TYR cc_start: 0.8874 (t80) cc_final: 0.8616 (t80)
REVERT: A  725 PHE cc_start: 0.8534 (t80) cc_final: 0.8147 (t80)
REVERT: A  738 ILE cc_start: 0.7299 (mt) cc_final: 0.7042 (mt)
REVERT: A  781 GLU cc_start: 0.8348 (tt0) cc_final: 0.7774 (tp30)
REVERT: A  796 GLU cc_start: 0.8879 (tt0) cc_final: 0.8168 (tm-30)
REVERT: A  798 ASN cc_start: 0.8001 (p0) cc_final: 0.7217 (t0)
REVERT: A  927 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8911 (m-10)
REVERT: A  950 TRP cc_start: 0.8769 (t-100) cc_final: 0.8473 (t-100)
REVERT: A 1033 GLU cc_start: 0.8985 (pm20) cc_final: 0.8767 (pm20)
REVERT: A 1043 SER cc_start: 0.9432 (m) cc_final: 0.9115 (t)
REVERT: A 1112 MET cc_start: 0.8407 (ppp) cc_final: 0.7962 (ppp)
  outliers start: 2
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1443
  time to fit residues: 43.6108
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 837 GLN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.136939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115039 restraints weight = 13863.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.118445 restraints weight = 8470.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120829 restraints weight = 5775.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6698  Z= 0.211
  Angle     :  0.719  10.666   9138  Z= 0.370
  Chirality :  0.044   0.188   1076
  Planarity :  0.004   0.037   1104
  Dihedral  :  8.318  52.879   1248
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.45 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.41 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.28), residues: 804
  helix:  0.01 (0.23), residues: 489
  sheet:  None (None), residues: 0
  loop : -4.19 (0.28), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 826 
 HIS   0.008   0.001   HIS A 590 
 PHE   0.026   0.002   PHE A 839 
 TYR   0.015   0.002   TYR A 645 
 ARG   0.001   0.000   ARG A 233 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.9082 (t0) cc_final: 0.8841 (t0)
REVERT: A  220 LEU cc_start: 0.8876 (pp) cc_final: 0.8502 (pp)
REVERT: A  221 LEU cc_start: 0.9359 (tp) cc_final: 0.8896 (tp)
REVERT: A  233 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8132 (mtt-85)
REVERT: A  302 ARG cc_start: 0.7314 (ptt-90) cc_final: 0.6975 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6565 (tpt-90)
REVERT: A  453 MET cc_start: 0.5067 (pmm) cc_final: 0.3871 (pmm)
REVERT: A  465 MET cc_start: 0.8350 (ttt) cc_final: 0.7901 (tmm)
REVERT: A  536 ILE cc_start: 0.9188 (mm) cc_final: 0.8871 (mm)
REVERT: A  573 ASP cc_start: 0.8565 (m-30) cc_final: 0.8331 (m-30)
REVERT: A  578 CYS cc_start: 0.9412 (m) cc_final: 0.9051 (m)
REVERT: A  581 TRP cc_start: 0.8797 (t-100) cc_final: 0.7767 (t-100)
REVERT: A  584 THR cc_start: 0.9566 (p) cc_final: 0.9221 (p)
REVERT: A  587 ASP cc_start: 0.8821 (p0) cc_final: 0.8127 (m-30)
REVERT: A  596 THR cc_start: 0.9357 (p) cc_final: 0.9031 (p)
REVERT: A  597 VAL cc_start: 0.9667 (p) cc_final: 0.9406 (p)
REVERT: A  636 TYR cc_start: 0.8780 (t80) cc_final: 0.8468 (t80)
REVERT: A  725 PHE cc_start: 0.8400 (t80) cc_final: 0.7865 (t80)
REVERT: A  781 GLU cc_start: 0.8371 (tt0) cc_final: 0.7773 (tp30)
REVERT: A  791 TRP cc_start: 0.8471 (m-10) cc_final: 0.8223 (m-10)
REVERT: A  796 GLU cc_start: 0.8827 (tt0) cc_final: 0.8083 (tm-30)
REVERT: A  798 ASN cc_start: 0.7789 (p0) cc_final: 0.6934 (t0)
REVERT: A  895 MET cc_start: -0.0450 (mmt) cc_final: -0.1324 (mtp)
REVERT: A  972 GLU cc_start: 0.8581 (tt0) cc_final: 0.8211 (tt0)
REVERT: A 1083 MET cc_start: 0.9020 (mmp) cc_final: 0.8411 (mmp)
REVERT: A 1112 MET cc_start: 0.8475 (ppp) cc_final: 0.8035 (ppp)
REVERT: A 1113 MET cc_start: 0.8571 (ttp) cc_final: 0.7715 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1412
  time to fit residues: 42.2005
Evaluate side-chains
  171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0570
   chunk 27 optimal weight:    0.4980
   chunk 53 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0770
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
A 590 HIS
A 644 ASN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.119357 restraints weight = 14301.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.123040 restraints weight = 8696.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.125576 restraints weight = 5877.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6698  Z= 0.183
  Angle     :  0.693   8.041   9138  Z= 0.357
  Chirality :  0.043   0.178   1076
  Planarity :  0.004   0.040   1104
  Dihedral  :  7.981  58.174   1248
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.33 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.29), residues: 804
  helix:  0.16 (0.23), residues: 490
  sheet: -5.26 (0.55), residues: 16
  loop : -3.98 (0.31), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1032 
 HIS   0.006   0.001   HIS A 590 
 PHE   0.020   0.002   PHE A 839 
 TYR   0.036   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A 547 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8738 (pp) cc_final: 0.8410 (pp)
REVERT: A  221 LEU cc_start: 0.9368 (tp) cc_final: 0.8797 (tp)
REVERT: A  233 ARG cc_start: 0.8837 (mtt180) cc_final: 0.7623 (mtt-85)
REVERT: A  383 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6537 (tpt-90)
REVERT: A  453 MET cc_start: 0.4990 (pmm) cc_final: 0.3726 (pmm)
REVERT: A  465 MET cc_start: 0.8238 (ttt) cc_final: 0.8025 (tmm)
REVERT: A  530 MET cc_start: 0.9411 (tpt) cc_final: 0.9203 (tpt)
REVERT: A  536 ILE cc_start: 0.9052 (mm) cc_final: 0.8734 (mm)
REVERT: A  557 PHE cc_start: 0.9134 (p90) cc_final: 0.8891 (p90)
REVERT: A  578 CYS cc_start: 0.9359 (m) cc_final: 0.9008 (m)
REVERT: A  581 TRP cc_start: 0.8781 (t-100) cc_final: 0.7765 (t-100)
REVERT: A  587 ASP cc_start: 0.8730 (p0) cc_final: 0.8109 (m-30)
REVERT: A  596 THR cc_start: 0.9388 (p) cc_final: 0.9032 (p)
REVERT: A  597 VAL cc_start: 0.9683 (p) cc_final: 0.9413 (p)
REVERT: A  608 MET cc_start: 0.8869 (mtt) cc_final: 0.8581 (mtt)
REVERT: A  645 TYR cc_start: 0.9342 (t80) cc_final: 0.9107 (t80)
REVERT: A  725 PHE cc_start: 0.8443 (t80) cc_final: 0.7807 (t80)
REVERT: A  798 ASN cc_start: 0.7703 (p0) cc_final: 0.6797 (t0)
REVERT: A  811 THR cc_start: 0.8087 (p) cc_final: 0.7740 (p)
REVERT: A  970 ASN cc_start: 0.8282 (p0) cc_final: 0.8044 (p0)
REVERT: A  974 TYR cc_start: 0.8597 (t80) cc_final: 0.8313 (t80)
REVERT: A 1033 GLU cc_start: 0.8486 (pm20) cc_final: 0.8209 (pm20)
REVERT: A 1083 MET cc_start: 0.9157 (mmp) cc_final: 0.8061 (mmp)
REVERT: A 1112 MET cc_start: 0.8559 (ppp) cc_final: 0.8209 (ppp)
REVERT: A 1113 MET cc_start: 0.8623 (ttp) cc_final: 0.7701 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1381
  time to fit residues: 42.4266
Evaluate side-chains
  172 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 81 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A1128 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 = 0.3785 r_free = 0.3785 target = 0.142725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.121840 restraints weight = 14007.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.124751 restraints weight = 9157.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.126826 restraints weight = 6537.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6698  Z= 0.193
  Angle     :  0.679   7.527   9138  Z= 0.352
  Chirality :  0.042   0.191   1076
  Planarity :  0.004   0.039   1104
  Dihedral  :  7.966  58.195   1248
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.20 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.29), residues: 804
  helix:  0.36 (0.23), residues: 488
  sheet: -4.96 (0.63), residues: 16
  loop : -3.81 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 791 
 HIS   0.003   0.000   HIS A 590 
 PHE   0.026   0.002   PHE A 554 
 TYR   0.038   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A1132 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9383 (tp) cc_final: 0.8988 (tp)
REVERT: A  228 THR cc_start: 0.8952 (p) cc_final: 0.8438 (p)
REVERT: A  232 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7807 (mm-40)
REVERT: A  302 ARG cc_start: 0.7166 (ptt-90) cc_final: 0.6862 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7723 (mtt180) cc_final: 0.6510 (tpt-90)
REVERT: A  453 MET cc_start: 0.4912 (pmm) cc_final: 0.3738 (pmm)
REVERT: A  465 MET cc_start: 0.8268 (ttt) cc_final: 0.7819 (tmm)
REVERT: A  530 MET cc_start: 0.9264 (tpt) cc_final: 0.8970 (tpp)
REVERT: A  536 ILE cc_start: 0.8999 (mm) cc_final: 0.8648 (mm)
REVERT: A  557 PHE cc_start: 0.9174 (p90) cc_final: 0.8824 (p90)
REVERT: A  578 CYS cc_start: 0.9277 (m) cc_final: 0.8880 (m)
REVERT: A  581 TRP cc_start: 0.8743 (t-100) cc_final: 0.7713 (t-100)
REVERT: A  584 THR cc_start: 0.9531 (p) cc_final: 0.9229 (p)
REVERT: A  587 ASP cc_start: 0.8702 (p0) cc_final: 0.8016 (m-30)
REVERT: A  596 THR cc_start: 0.9316 (p) cc_final: 0.8973 (p)
REVERT: A  597 VAL cc_start: 0.9627 (p) cc_final: 0.9325 (p)
REVERT: A  608 MET cc_start: 0.8796 (mtt) cc_final: 0.8434 (mtt)
REVERT: A  725 PHE cc_start: 0.8091 (t80) cc_final: 0.7888 (t80)
REVERT: A  798 ASN cc_start: 0.7570 (p0) cc_final: 0.6477 (t0)
REVERT: A  810 LEU cc_start: 0.8905 (pt) cc_final: 0.8572 (pp)
REVERT: A  970 ASN cc_start: 0.8214 (p0) cc_final: 0.7960 (p0)
REVERT: A  974 TYR cc_start: 0.8448 (t80) cc_final: 0.8172 (t80)
REVERT: A 1007 ILE cc_start: 0.8647 (tt) cc_final: 0.8133 (tp)
REVERT: A 1090 THR cc_start: 0.9216 (m) cc_final: 0.8993 (t)
REVERT: A 1112 MET cc_start: 0.8330 (ppp) cc_final: 0.7796 (ppp)
REVERT: A 1113 MET cc_start: 0.8382 (ttp) cc_final: 0.7584 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1393
  time to fit residues: 41.2807
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 75 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 837 GLN
A 858 GLN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.143845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121748 restraints weight = 13897.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125208 restraints weight = 8622.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.127660 restraints weight = 5894.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6698  Z= 0.184
  Angle     :  0.682   8.125   9138  Z= 0.352
  Chirality :  0.043   0.197   1076
  Planarity :  0.004   0.043   1104
  Dihedral  :  7.762  59.280   1248
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.08 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.29), residues: 804
  helix:  0.38 (0.23), residues: 483
  sheet: -4.82 (0.71), residues: 16
  loop : -3.68 (0.32), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 791 
 HIS   0.003   0.001   HIS A 429 
 PHE   0.019   0.002   PHE A 554 
 TYR   0.055   0.002   TYR A1011 
 ARG   0.001   0.000   ARG A 233 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9363 (tp) cc_final: 0.8997 (tp)
REVERT: A  302 ARG cc_start: 0.7135 (ptt-90) cc_final: 0.6900 (ptt-90)
REVERT: A  383 ARG cc_start: 0.7750 (mtt180) cc_final: 0.6529 (tpp-160)
REVERT: A  453 MET cc_start: 0.4830 (pmm) cc_final: 0.3751 (pmm)
REVERT: A  465 MET cc_start: 0.8426 (ttt) cc_final: 0.7559 (tmm)
REVERT: A  518 MET cc_start: 0.8609 (ttm) cc_final: 0.8156 (tpp)
REVERT: A  530 MET cc_start: 0.9335 (tpt) cc_final: 0.9018 (tpp)
REVERT: A  557 PHE cc_start: 0.9207 (p90) cc_final: 0.8841 (p90)
REVERT: A  578 CYS cc_start: 0.9259 (m) cc_final: 0.9049 (m)
REVERT: A  581 TRP cc_start: 0.8752 (t-100) cc_final: 0.7766 (t-100)
REVERT: A  584 THR cc_start: 0.9562 (p) cc_final: 0.9251 (p)
REVERT: A  587 ASP cc_start: 0.8660 (p0) cc_final: 0.8103 (m-30)
REVERT: A  596 THR cc_start: 0.9356 (p) cc_final: 0.9064 (p)
REVERT: A  597 VAL cc_start: 0.9640 (p) cc_final: 0.9409 (p)
REVERT: A  608 MET cc_start: 0.8897 (mtt) cc_final: 0.8632 (mtt)
REVERT: A  725 PHE cc_start: 0.8209 (t80) cc_final: 0.7726 (t80)
REVERT: A  798 ASN cc_start: 0.7709 (p0) cc_final: 0.6707 (t0)
REVERT: A  811 THR cc_start: 0.7869 (p) cc_final: 0.7627 (p)
REVERT: A 1083 MET cc_start: 0.9069 (mmp) cc_final: 0.8689 (mmm)
REVERT: A 1112 MET cc_start: 0.8343 (ppp) cc_final: 0.7838 (ppp)
REVERT: A 1113 MET cc_start: 0.8542 (ttp) cc_final: 0.7712 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1358
  time to fit residues: 38.9905
Evaluate side-chains
  162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 59 optimal weight:    0.3980
   chunk 63 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0070
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.2402

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 858 GLN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.142608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.121634 restraints weight = 14301.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.124500 restraints weight = 9455.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126663 restraints weight = 6775.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6698  Z= 0.199
  Angle     :  0.698   8.469   9138  Z= 0.360
  Chirality :  0.044   0.210   1076
  Planarity :  0.005   0.043   1104
  Dihedral  :  7.788  59.551   1248
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.45 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.29), residues: 804
  helix:  0.45 (0.24), residues: 485
  sheet: -4.24 (1.21), residues: 10
  loop : -3.70 (0.30), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 791 
 HIS   0.004   0.001   HIS A1055 
 PHE   0.022   0.002   PHE A 725 
 TYR   0.029   0.002   TYR A 645 
 ARG   0.004   0.000   ARG A 233 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 LEU cc_start: 0.9384 (tp) cc_final: 0.9034 (tp)
REVERT: A  383 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6614 (tpt170)
REVERT: A  465 MET cc_start: 0.8378 (ttt) cc_final: 0.7657 (tmm)
REVERT: A  518 MET cc_start: 0.8668 (ttm) cc_final: 0.8196 (tpp)
REVERT: A  557 PHE cc_start: 0.9224 (p90) cc_final: 0.8825 (p90)
REVERT: A  578 CYS cc_start: 0.9391 (m) cc_final: 0.9049 (m)
REVERT: A  581 TRP cc_start: 0.8775 (t-100) cc_final: 0.8552 (t-100)
REVERT: A  587 ASP cc_start: 0.8747 (p0) cc_final: 0.8162 (m-30)
REVERT: A  608 MET cc_start: 0.8669 (mtt) cc_final: 0.8461 (mtt)
REVERT: A  725 PHE cc_start: 0.8396 (t80) cc_final: 0.7777 (t80)
REVERT: A  742 MET cc_start: 0.6771 (tmm) cc_final: 0.6488 (tmm)
REVERT: A  781 GLU cc_start: 0.8293 (tt0) cc_final: 0.7824 (tm-30)
REVERT: A  796 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8180 (tm-30)
REVERT: A  798 ASN cc_start: 0.7654 (p0) cc_final: 0.6722 (t0)
REVERT: A  811 THR cc_start: 0.7823 (p) cc_final: 0.7606 (p)
REVERT: A 1007 ILE cc_start: 0.8386 (tt) cc_final: 0.7756 (tp)
REVERT: A 1083 MET cc_start: 0.9105 (mmp) cc_final: 0.8284 (ttm)
REVERT: A 1112 MET cc_start: 0.8284 (ppp) cc_final: 0.7806 (ppp)
REVERT: A 1113 MET cc_start: 0.8446 (ttp) cc_final: 0.7613 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.1375
  time to fit residues: 38.9662
Evaluate side-chains
  163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 622 ASN
** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.139350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116611 restraints weight = 14225.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.120115 restraints weight = 8742.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.122633 restraints weight = 5967.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.5025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6698  Z= 0.226
  Angle     :  0.725   8.712   9138  Z= 0.374
  Chirality :  0.045   0.211   1076
  Planarity :  0.005   0.047   1104
  Dihedral  :  7.837  57.944   1248
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.20 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.29), residues: 804
  helix:  0.39 (0.23), residues: 490
  sheet: -4.53 (0.87), residues: 18
  loop : -3.91 (0.30), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 791 
 HIS   0.003   0.001   HIS A 759 
 PHE   0.020   0.002   PHE A1127 
 TYR   0.027   0.002   TYR A1011 
 ARG   0.003   0.000   ARG A 233 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8906 (pp) cc_final: 0.8680 (pp)
REVERT: A  221 LEU cc_start: 0.9393 (tp) cc_final: 0.9055 (tp)
REVERT: A  383 ARG cc_start: 0.7811 (mtt180) cc_final: 0.6628 (tpt90)
REVERT: A  465 MET cc_start: 0.8409 (ttt) cc_final: 0.7678 (tmm)
REVERT: A  536 ILE cc_start: 0.9101 (mm) cc_final: 0.8735 (mm)
REVERT: A  578 CYS cc_start: 0.9497 (m) cc_final: 0.9236 (m)
REVERT: A  581 TRP cc_start: 0.8934 (t-100) cc_final: 0.8693 (t-100)
REVERT: A  584 THR cc_start: 0.9579 (p) cc_final: 0.9235 (p)
REVERT: A  587 ASP cc_start: 0.8744 (p0) cc_final: 0.8200 (m-30)
REVERT: A  645 TYR cc_start: 0.9352 (t80) cc_final: 0.9028 (t80)
REVERT: A  725 PHE cc_start: 0.8508 (t80) cc_final: 0.7888 (t80)
REVERT: A  742 MET cc_start: 0.6558 (tmm) cc_final: 0.6247 (tmm)
REVERT: A  781 GLU cc_start: 0.8340 (tt0) cc_final: 0.7571 (tp30)
REVERT: A  796 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8237 (tm-30)
REVERT: A  798 ASN cc_start: 0.7864 (p0) cc_final: 0.6939 (t0)
REVERT: A  824 GLN cc_start: 0.8334 (pp30) cc_final: 0.7821 (pm20)
REVERT: A 1007 ILE cc_start: 0.8438 (tt) cc_final: 0.7718 (tp)
REVERT: A 1083 MET cc_start: 0.8808 (mmp) cc_final: 0.8448 (ttm)
REVERT: A 1112 MET cc_start: 0.8398 (ppp) cc_final: 0.7980 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1381
  time to fit residues: 40.0324
Evaluate side-chains
  166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 622 ASN
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 858 GLN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.140184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.118429 restraints weight = 13646.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.122108 restraints weight = 8340.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124725 restraints weight = 5620.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6698  Z= 0.205
  Angle     :  0.722   9.922   9138  Z= 0.371
  Chirality :  0.045   0.214   1076
  Planarity :  0.005   0.046   1104
  Dihedral  :  7.744  56.278   1248
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.57 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.29), residues: 804
  helix:  0.39 (0.23), residues: 490
  sheet: -4.41 (1.01), residues: 18
  loop : -3.84 (0.30), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 651 
 HIS   0.006   0.001   HIS A1055 
 PHE   0.015   0.002   PHE A 839 
 TYR   0.028   0.002   TYR A1011 
 ARG   0.005   0.000   ARG A 302 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LEU cc_start: 0.8869 (pp) cc_final: 0.8555 (pp)
REVERT: A  221 LEU cc_start: 0.9353 (tp) cc_final: 0.8828 (tp)
REVERT: A  383 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6616 (tpp-160)
REVERT: A  465 MET cc_start: 0.8424 (ttt) cc_final: 0.7743 (tmm)
REVERT: A  536 ILE cc_start: 0.9073 (mm) cc_final: 0.8711 (mm)
REVERT: A  578 CYS cc_start: 0.9442 (m) cc_final: 0.9222 (m)
REVERT: A  581 TRP cc_start: 0.8891 (t-100) cc_final: 0.8644 (t-100)
REVERT: A  584 THR cc_start: 0.9556 (p) cc_final: 0.9197 (p)
REVERT: A  587 ASP cc_start: 0.8682 (p0) cc_final: 0.8187 (m-30)
REVERT: A  725 PHE cc_start: 0.8596 (t80) cc_final: 0.7980 (t80)
REVERT: A  742 MET cc_start: 0.6548 (tmm) cc_final: 0.6255 (tmm)
REVERT: A  781 GLU cc_start: 0.8359 (tt0) cc_final: 0.7801 (tm-30)
REVERT: A  796 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8233 (tm-30)
REVERT: A  798 ASN cc_start: 0.7899 (p0) cc_final: 0.6986 (t0)
REVERT: A  811 THR cc_start: 0.8239 (p) cc_final: 0.8026 (p)
REVERT: A  824 GLN cc_start: 0.8341 (pp30) cc_final: 0.7861 (pm20)
REVERT: A  895 MET cc_start: -0.0178 (mtt) cc_final: -0.0850 (mtt)
REVERT: A 1083 MET cc_start: 0.9134 (mmp) cc_final: 0.8400 (ttm)
REVERT: A 1113 MET cc_start: 0.8668 (ttp) cc_final: 0.7827 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1382
  time to fit residues: 37.8981
Evaluate side-chains
  162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 363 ASN
A 622 ASN
A 824 GLN
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.115546 restraints weight = 13702.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.119306 restraints weight = 8227.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.121945 restraints weight = 5499.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.5253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6698  Z= 0.245
  Angle     :  0.757  10.641   9138  Z= 0.390
  Chirality :  0.046   0.209   1076
  Planarity :  0.005   0.048   1104
  Dihedral  :  7.965  58.384   1248
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.95 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.75 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.29), residues: 804
  helix:  0.29 (0.23), residues: 489
  sheet: -4.26 (1.04), residues: 18
  loop : -3.89 (0.30), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 651 
 HIS   0.006   0.001   HIS A1055 
 PHE   0.027   0.002   PHE A1111 
 TYR   0.025   0.002   TYR A1011 
 ARG   0.004   0.000   ARG A 302 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 LEU cc_start: 0.8492 (mm) cc_final: 0.8219 (tp)
REVERT: A  220 LEU cc_start: 0.8935 (pp) cc_final: 0.8712 (pp)
REVERT: A  221 LEU cc_start: 0.9363 (tp) cc_final: 0.9083 (tp)
REVERT: A  383 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6691 (tpt90)
REVERT: A  465 MET cc_start: 0.8461 (ttt) cc_final: 0.7729 (tmm)
REVERT: A  518 MET cc_start: 0.8860 (ttm) cc_final: 0.8439 (tpp)
REVERT: A  536 ILE cc_start: 0.9156 (mm) cc_final: 0.8737 (mm)
REVERT: A  578 CYS cc_start: 0.9494 (m) cc_final: 0.9286 (m)
REVERT: A  584 THR cc_start: 0.9568 (p) cc_final: 0.9222 (p)
REVERT: A  587 ASP cc_start: 0.8726 (p0) cc_final: 0.8236 (m-30)
REVERT: A  710 LEU cc_start: 0.9222 (mp) cc_final: 0.9022 (mp)
REVERT: A  742 MET cc_start: 0.6661 (tmm) cc_final: 0.6315 (tmm)
REVERT: A  796 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8240 (tm-30)
REVERT: A  798 ASN cc_start: 0.8039 (p0) cc_final: 0.7231 (t0)
REVERT: A  811 THR cc_start: 0.8385 (p) cc_final: 0.8166 (p)
REVERT: A  824 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7920 (pm20)
REVERT: A  895 MET cc_start: 0.0117 (mtt) cc_final: -0.0622 (mtt)
REVERT: A  955 LEU cc_start: 0.8617 (mm) cc_final: 0.8413 (pp)
REVERT: A 1030 LEU cc_start: 0.8737 (mm) cc_final: 0.8368 (tp)
REVERT: A 1034 LEU cc_start: 0.8130 (mm) cc_final: 0.7898 (mm)
REVERT: A 1083 MET cc_start: 0.9138 (mmp) cc_final: 0.8356 (ttm)
REVERT: A 1113 MET cc_start: 0.8821 (ttp) cc_final: 0.7956 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1365
  time to fit residues: 37.9353
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0870
   chunk 11 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   overall best weight:    0.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 324 ASN
A 363 ASN
A 622 ASN
A 659 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.143686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.121140 restraints weight = 13969.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.124890 restraints weight = 8537.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127573 restraints weight = 5763.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.5581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6698  Z= 0.195
  Angle     :  0.738  10.726   9138  Z= 0.377
  Chirality :  0.046   0.226   1076
  Planarity :  0.005   0.052   1104
  Dihedral  :  7.613  56.854   1248
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.07 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.29), residues: 804
  helix:  0.33 (0.23), residues: 479
  sheet: -4.11 (1.06), residues: 18
  loop : -3.59 (0.31), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 651 
 HIS   0.005   0.001   HIS A1055 
 PHE   0.023   0.002   PHE A1111 
 TYR   0.023   0.002   TYR A1011 
 ARG   0.005   0.000   ARG A 892 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1977.93 seconds
wall clock time: 36 minutes 14.58 seconds (2174.58 seconds total)