Starting phenix.real_space_refine
on Thu Mar 13 03:15:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmq_22261/03_2025/6xmq_22261.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    5410      2.51       5
     N    1375      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8362
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1085, 8330
          Classifications: {'peptide': 1085}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 48, 'TRANS': 1036}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 142
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.97, per 1000 atoms: 0.59
  Number of scatterers: 8362
  At special positions: 0
  Unit cell: (84.49, 95.2, 136.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P       3     15.00
     Mg      1     11.99
     O    1536      8.00
     N    1375      7.00
     C    5410      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: 2.29
  Conformation dependent library (CDL) restraints added in 962.3 milliseconds
  

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      48.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 44
      removed outlier: 3.595A  pdb=" N   PHE A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      Proline residue:  A  34  - end of helix
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 3.701A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 78 through 86
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 3.830A  pdb=" N   GLU A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 163
      removed outlier: 3.956A  pdb=" N   GLN A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 188 through 198
      removed outlier: 3.880A  pdb=" N   VAL A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 215
    Processing helix  chain 'A' and resid 218 through 247
      removed outlier: 3.524A  pdb=" N   ARG A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 372 through 375
      removed outlier: 3.791A  pdb=" N   GLU A 375 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 372 through 375'
    Processing helix  chain 'A' and resid 376 through 387
    Processing helix  chain 'A' and resid 396 through 424
      removed outlier: 3.813A  pdb=" N   LEU A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 443
      removed outlier: 4.536A  pdb=" N   LEU A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A 443 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 463
      removed outlier: 4.096A  pdb=" N   MET A 453 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 473
      No H-bonds generated for 'chain 'A' and resid 471 through 473'
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 4.258A  pdb=" N   ARG A 480 " --> pdb=" O   PRO A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.717A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY A 530 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 606 through 611
    Processing helix  chain 'A' and resid 620 through 630
      removed outlier: 3.848A  pdb=" N   TYR A 625 " --> pdb=" O   TYR A 621 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS A 626 " --> pdb=" O   ASP A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 689
      removed outlier: 3.659A  pdb=" N   THR A 682 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS A 684 " --> pdb=" O   ILE A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 712
      removed outlier: 3.512A  pdb=" N   ALA A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 758
    Processing helix  chain 'A' and resid 767 through 773
    Processing helix  chain 'A' and resid 778 through 786
      removed outlier: 3.697A  pdb=" N   ARG A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   HIS A 785 " --> pdb=" O   ASP A 781 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 786 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 808
      removed outlier: 3.743A  pdb=" N   GLY A 808 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 819
      No H-bonds generated for 'chain 'A' and resid 817 through 819'
    Processing helix  chain 'A' and resid 820 through 827
    Processing helix  chain 'A' and resid 837 through 851
    Processing helix  chain 'A' and resid 972 through 1012
      removed outlier: 4.370A  pdb=" N   ALA A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1036
      removed outlier: 4.107A  pdb=" N   CYS A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   SER A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1084
    Processing helix  chain 'A' and resid 1099 through 1121
      removed outlier: 4.139A  pdb=" N   PHE A1117 " --> pdb=" O   GLN A1113 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A1118 " --> pdb=" O   VAL A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1152
      removed outlier: 3.889A  pdb=" N   TYR A1137 " --> pdb=" O   ASN A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1162
      removed outlier: 3.996A  pdb=" N   ASN A1159 " --> pdb=" O   LEU A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1198
      removed outlier: 4.114A  pdb=" N   ILE A1173 " --> pdb=" O   ASP A1169 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A1179 " --> pdb=" O   LEU A1175 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET A1198 " --> pdb=" O   LYS A1194 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.640A  pdb=" N   VAL A 143 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.801A  pdb=" N   TYR A 102 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   SER A  15 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU A 100 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   LEU A  17 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   HIS A  98 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 111 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120
    Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130
      removed outlier: 3.565A  pdb=" N   PHE A 130 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 267
      removed outlier: 4.715A  pdb=" N   ASN A 257 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 279 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   LEU A 277 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A 366 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A 296 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASP A 292 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317
      removed outlier: 6.682A  pdb=" N   SER A 299 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL A 348 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 469
      removed outlier: 6.729A  pdb=" N   GLY A 830 " --> pdb=" O   PHE A 964 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   SER A 966 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 966 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 829 " --> pdb=" O   THR A 811 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP A 487 " --> pdb=" O   CYS A 814 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   CYS A 484 " --> pdb=" O   ILE A 694 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ILE A 696 " --> pdb=" O   CYS A 484 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   PHE A 486 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   TYR A 789 " --> pdb=" O   SER A 693 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   MET A 695 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LEU A 719 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   THR A 766 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU A 721 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516
      removed outlier: 3.642A  pdb=" N   VAL A 498 " --> pdb=" O   HIS A 672 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ILE A 670 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 502 " --> pdb=" O   PHE A 668 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   PHE A 668 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   PHE A 665 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   SER A 640 " --> pdb=" O   PHE A 665 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 600 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG A 578 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER A 594 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE A 576 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 536 through 537
      removed outlier: 3.880A  pdb=" N   VAL A 536 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    403 hydrogen bonds defined for protein.
    1182 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: 2.97

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2661
        1.35 -     1.48: 2089
        1.48 -     1.60: 3725
        1.60 -     1.73: 4
        1.73 -     1.86: 64
  Bond restraints: 8543
  Sorted by residual:
  bond pdb=" C1' ACP A1301 "
       pdb=" O4' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.390  1.615 -0.225 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C1' ACP A1301 "
       pdb=" C2' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.527  1.304  0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" C4' ACP A1301 "
       pdb=" O4' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.428  1.301  0.127 2.00e-02 2.50e+03 4.04e+01
  bond pdb=" C6  ACP A1301 "
       pdb=" N6  ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.335  1.448 -0.113 2.00e-02 2.50e+03 3.21e+01
  bond pdb=" C2' ACP A1301 "
       pdb=" O2' ACP A1301 "
    ideal  model  delta    sigma   weight residual
    1.401  1.490 -0.089 2.00e-02 2.50e+03 1.99e+01
  ... (remaining 8538 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 11500
        2.65 -     5.30: 99
        5.30 -     7.95: 3
        7.95 -    10.60: 7
       10.60 -    13.25: 1
  Bond angle restraints: 11610
  Sorted by residual:
  angle pdb=" O3A ACP A1301 "
        pdb=" PA  ACP A1301 "
        pdb=" O5' ACP A1301 "
      ideal   model   delta    sigma   weight residual
      93.75  107.00  -13.25 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" N1  ACP A1301 "
        pdb=" C6  ACP A1301 "
        pdb=" N6  ACP A1301 "
      ideal   model   delta    sigma   weight residual
     119.32  108.84   10.48 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" C3B ACP A1301 "
        pdb=" PB  ACP A1301 "
        pdb=" O3A ACP A1301 "
      ideal   model   delta    sigma   weight residual
      98.05  108.34  -10.29 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" O1B ACP A1301 "
        pdb=" PB  ACP A1301 "
        pdb=" O2B ACP A1301 "
      ideal   model   delta    sigma   weight residual
     119.60  110.06    9.54 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" O1A ACP A1301 "
        pdb=" PA  ACP A1301 "
        pdb=" O2A ACP A1301 "
      ideal   model   delta    sigma   weight residual
     118.95  110.47    8.48 3.00e+00 1.11e-01 7.99e+00
  ... (remaining 11605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.49: 4751
       18.49 -    36.98: 313
       36.98 -    55.46: 31
       55.46 -    73.95: 13
       73.95 -    92.44: 8
  Dihedral angle restraints: 5116
    sinusoidal: 1964
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" O1B ACP A1301 "
           pdb=" C3B ACP A1301 "
           pdb=" PB  ACP A1301 "
           pdb=" PG  ACP A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.82   39.62  -92.44     1      3.00e+01 1.11e-03 1.11e+01
  dihedral pdb=" CB  GLU A 420 "
           pdb=" CG  GLU A 420 "
           pdb=" CD  GLU A 420 "
           pdb=" OE1 GLU A 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.81  -89.81     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 520 "
           pdb=" CG  GLU A 520 "
           pdb=" CD  GLU A 520 "
           pdb=" OE1 GLU A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.40  -89.40     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1163
       0.057 -    0.114: 180
       0.114 -    0.171: 18
       0.171 -    0.227: 0
       0.227 -    0.284: 1
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" C2' ACP A1301 "
            pdb=" C1' ACP A1301 "
            pdb=" C3' ACP A1301 "
            pdb=" O2' ACP A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.47   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ILE A 301 "
            pdb=" N   ILE A 301 "
            pdb=" C   ILE A 301 "
            pdb=" CB  ILE A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1359 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1039 "    0.023 5.00e-02 4.00e+02   3.55e-02 2.02e+00
        pdb=" N   PRO A1040 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A1040 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1040 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 273 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO A 274 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 274 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 274 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 962 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO A 963 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 963 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 963 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 18
        2.31 -     2.96: 3914
        2.96 -     3.60: 11684
        3.60 -     4.25: 16694
        4.25 -     4.90: 28749
  Nonbonded interactions: 61059
  Sorted by model distance:
  nonbonded pdb=" O3G ACP A1301 "
            pdb="MG    MG A1302 "
     model   vdw
     1.660 2.170
  nonbonded pdb=" OD2 ASP A 816 "
            pdb="MG    MG A1302 "
     model   vdw
     2.005 2.170
  nonbonded pdb=" OD2 ASP A 487 "
            pdb="MG    MG A1302 "
     model   vdw
     2.042 2.170
  nonbonded pdb=" OD2 ASP A 487 "
            pdb=" O3G ACP A1301 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OD1 ASP A 816 "
            pdb="MG    MG A1302 "
     model   vdw
     2.102 2.170
  ... (remaining 61054 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.960
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
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      :  0.006   0.225   8543  Z= 0.407
  Angle     :  0.662  13.253  11610  Z= 0.343
  Chirality :  0.042   0.284   1362
  Planarity :  0.004   0.036   1460
  Dihedral  : 13.161  92.440   3074
  Min Nonbonded Distance : 1.660

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.23), residues: 1077
  helix: -0.19 (0.21), residues: 489
  sheet: -1.75 (0.40), residues: 132
  loop : -1.80 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.016   0.002   PHE A 237 
 TYR   0.013   0.001   TYR A 625 
 ARG   0.004   0.000   ARG A 613 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.993 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2090
  time to fit residues: 20.3815
Evaluate side-chains
  36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 166 HIS
A 514 HIS
** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 706 HIS
A 776 HIS
A 785 HIS
A 826 GLN
A 987 ASN
A1069 HIS
A1122 GLN
A1209 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.070996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.059396 restraints weight = 31008.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.061242 restraints weight = 16641.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.062412 restraints weight = 11109.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8543  Z= 0.255
  Angle     :  0.553   7.648  11610  Z= 0.288
  Chirality :  0.040   0.144   1362
  Planarity :  0.004   0.032   1460
  Dihedral  :  6.983  80.229   1178
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.57 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1077
  helix:  1.33 (0.23), residues: 490
  sheet: -1.58 (0.40), residues: 146
  loop : -1.31 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A1016 
 TYR   0.014   0.001   TYR A1010 
 ARG   0.003   0.000   ARG A1037 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  239 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8810 (tpt170)
REVERT: A  246 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8252 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1799
  time to fit residues: 13.5006
Evaluate side-chains
  44 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 55 optimal weight:   30.0000
   chunk 58 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 327 ASN
** A 533 HIS ** 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 = 0.3362 r_free = 0.3362 target = 0.068305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.056361 restraints weight = 31780.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.058160 restraints weight = 17185.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.059334 restraints weight = 11609.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   8543  Z= 0.364
  Angle     :  0.614   7.499  11610  Z= 0.317
  Chirality :  0.041   0.145   1362
  Planarity :  0.004   0.032   1460
  Dihedral  :  6.811  82.198   1178
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.51 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.26), residues: 1077
  helix:  1.73 (0.24), residues: 484
  sheet: -1.33 (0.42), residues: 142
  loop : -1.14 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 691 
 PHE   0.017   0.002   PHE A 499 
 TYR   0.014   0.001   TYR A 625 
 ARG   0.004   0.000   ARG A 634 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (t80)
REVERT: A  807 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8534 (mtm)
REVERT: A 1162 MET cc_start: 0.9135 (mmm) cc_final: 0.8601 (tpt)
  outliers start: 16
  outliers final: 10
  residues processed: 46
  average time/residue: 0.1687
  time to fit residues: 12.3170
Evaluate side-chains
  46 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  807 MET
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.069078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.057023 restraints weight = 31453.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.058865 restraints weight = 16785.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.060140 restraints weight = 11293.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8543  Z= 0.273
  Angle     :  0.543   7.595  11610  Z= 0.281
  Chirality :  0.040   0.144   1362
  Planarity :  0.003   0.034   1460
  Dihedral  :  6.673  89.793   1178
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.77 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1077
  helix:  2.02 (0.24), residues: 484
  sheet: -1.21 (0.43), residues: 141
  loop : -1.03 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 137 
 HIS   0.004   0.001   HIS A 691 
 PHE   0.014   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 625 
 ARG   0.003   0.000   ARG A 634 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 35
  time to evaluate  : 0.872 
Fit side-chains
  outliers start: 20
  outliers final: 14
  residues processed: 49
  average time/residue: 0.1386
  time to fit residues: 11.3460
Evaluate side-chains
  50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 533 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.069038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.057002 restraints weight = 31314.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.058854 restraints weight = 16742.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.060115 restraints weight = 11222.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8543  Z= 0.258
  Angle     :  0.531   6.537  11610  Z= 0.275
  Chirality :  0.039   0.144   1362
  Planarity :  0.003   0.032   1460
  Dihedral  :  6.398  83.688   1178
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.79 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1077
  helix:  2.14 (0.24), residues: 484
  sheet: -1.12 (0.44), residues: 141
  loop : -0.97 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 691 
 PHE   0.014   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 625 
 ARG   0.003   0.000   ARG A 634 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 38
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A  246 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8413 (t80)
REVERT: A  295 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8533 (mm)
  outliers start: 26
  outliers final: 18
  residues processed: 56
  average time/residue: 0.1364
  time to fit residues: 12.7364
Evaluate side-chains
  56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 36
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1022 THR
Chi-restraints excluded: chain A residue 1035 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 107 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.071059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.059525 restraints weight = 30835.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.061388 restraints weight = 16640.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062647 restraints weight = 11036.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8543  Z= 0.174
  Angle     :  0.500   9.153  11610  Z= 0.255
  Chirality :  0.038   0.143   1362
  Planarity :  0.003   0.033   1460
  Dihedral  :  6.118  76.016   1178
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.25 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1077
  helix:  2.41 (0.24), residues: 478
  sheet: -0.98 (0.44), residues: 141
  loop : -0.94 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.004   0.000   HIS A 533 
 PHE   0.011   0.001   PHE A 405 
 TYR   0.010   0.001   TYR A 625 
 ARG   0.001   0.000   ARG A 175 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 15
  residues processed: 54
  average time/residue: 0.1479
  time to fit residues: 13.3012
Evaluate side-chains
  53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.071082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.059233 restraints weight = 31327.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.061156 restraints weight = 16472.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.062461 restraints weight = 10885.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8543  Z= 0.144
  Angle     :  0.479   7.555  11610  Z= 0.245
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.938  72.336   1178
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.47 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 1077
  helix:  2.53 (0.25), residues: 478
  sheet: -0.82 (0.43), residues: 144
  loop : -0.89 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.002   0.000   HIS A 533 
 PHE   0.011   0.001   PHE A 246 
 TYR   0.009   0.001   TYR A1004 
 ARG   0.002   0.000   ARG A 247 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 MET cc_start: 0.8736 (mtp) cc_final: 0.8338 (mtm)
  outliers start: 20
  outliers final: 16
  residues processed: 56
  average time/residue: 0.1468
  time to fit residues: 13.5297
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    0.0470
   chunk 99 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    1.1082

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 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 = 0.3424 r_free = 0.3424 target = 0.070953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.059058 restraints weight = 31423.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.060980 restraints weight = 16531.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.062269 restraints weight = 10959.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8543  Z= 0.161
  Angle     :  0.493   8.981  11610  Z= 0.248
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.850  72.245   1178
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 21.37 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.26), residues: 1077
  helix:  2.54 (0.25), residues: 478
  sheet: -0.69 (0.43), residues: 141
  loop : -0.85 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.000   HIS A 533 
 PHE   0.009   0.001   PHE A 668 
 TYR   0.009   0.001   TYR A 625 
 ARG   0.001   0.000   ARG A 175 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 MET cc_start: 0.8701 (mtp) cc_final: 0.8298 (mtm)
  outliers start: 19
  outliers final: 16
  residues processed: 54
  average time/residue: 0.1392
  time to fit residues: 12.6812
Evaluate side-chains
  56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 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 = 0.3411 r_free = 0.3411 target = 0.070322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.058378 restraints weight = 31478.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.060272 restraints weight = 16609.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.061589 restraints weight = 11037.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8543  Z= 0.193
  Angle     :  0.512  11.357  11610  Z= 0.257
  Chirality :  0.038   0.142   1362
  Planarity :  0.003   0.030   1460
  Dihedral  :  5.866  72.970   1178
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.60 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1077
  helix:  2.50 (0.24), residues: 478
  sheet: -0.64 (0.43), residues: 141
  loop : -0.85 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.011   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 387 
 ARG   0.001   0.000   ARG A 260 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 MET cc_start: 0.8646 (mtp) cc_final: 0.8245 (mtm)
REVERT: A 1136 MET cc_start: 0.7666 (mmm) cc_final: 0.7335 (mmm)
  outliers start: 18
  outliers final: 16
  residues processed: 53
  average time/residue: 0.1366
  time to fit residues: 12.2534
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    0.0470
   chunk 4 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 73 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    0.1980
   overall best weight:    1.7682

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 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 = 0.3429 r_free = 0.3429 target = 0.070698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.059107 restraints weight = 31218.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.060960 restraints weight = 16672.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.062219 restraints weight = 11158.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8543  Z= 0.215
  Angle     :  0.526  12.279  11610  Z= 0.263
  Chirality :  0.038   0.143   1362
  Planarity :  0.003   0.030   1460
  Dihedral  :  5.898  72.811   1178
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.93 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1077
  helix:  2.45 (0.24), residues: 479
  sheet: -0.66 (0.43), residues: 141
  loop : -0.85 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 787 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.012   0.001   PHE A 499 
 TYR   0.014   0.001   TYR A1010 
 ARG   0.002   0.000   ARG A 634 

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 1.035 
Fit side-chains
  outliers start: 16
  outliers final: 16
  residues processed: 51
  average time/residue: 0.1453
  time to fit residues: 12.4677
Evaluate side-chains
  55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue 1009 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1146 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 72 optimal weight:    0.6980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 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 = 0.3413 r_free = 0.3413 target = 0.070377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.058447 restraints weight = 31579.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.060358 restraints weight = 16619.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.061665 restraints weight = 11021.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8543  Z= 0.177
  Angle     :  0.510  12.488  11610  Z= 0.255
  Chirality :  0.038   0.141   1362
  Planarity :  0.003   0.031   1460
  Dihedral  :  5.830  70.033   1178
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.93 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1077
  helix:  2.44 (0.24), residues: 479
  sheet: -0.61 (0.43), residues: 141
  loop : -0.83 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 137 
 HIS   0.003   0.000   HIS A 533 
 PHE   0.010   0.001   PHE A1016 
 TYR   0.020   0.001   TYR A1010 
 ARG   0.001   0.000   ARG A 634 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2174.09 seconds
wall clock time: 38 minutes 55.88 seconds (2335.88 seconds total)