Starting phenix.real_space_refine
on Fri Mar 14 07:55:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2025/7eei_31077.cif"
  }
  resolution = 3.6
  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=   0.004
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      65      5.16       5
     C    6290      2.51       5
     N    1723      2.21       5
     O    1747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "A ASP  337": not complete - not flipped    Residue "A ASP  444": not complete - not flipped    Residue "A ASP  640": not complete - not flipped    Residue "A GLU  702": not complete - not flipped  Time to flip 31 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: 9825
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1400, 9825
          Classifications: {'peptide': 1400}
          Incomplete info: {'backbone_only': 48, 'n_c_alpha_c_only': 14, 'truncation_to_alanine': 250}
          Link IDs: {'PTRANS': 58, 'TRANS': 1341}
          Unresolved chain links: 1
          Unresolved chain link angles: 29
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 1425
          Unresolved non-hydrogen angles: 1855
          Unresolved non-hydrogen dihedrals: 1090
          Unresolved non-hydrogen chiralities: 161
          Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 46, 'PHE:plan': 14, 'GLU:plan': 64, 'ARG:plan': 29}
          Unresolved non-hydrogen planarities: 799
  Time building chain proxies: 5.69, per 1000 atoms: 0.58
  Number of scatterers: 9825
  At special positions: 0
  Unit cell: (87.48, 112.32, 95.04, 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      65     16.00
     O    1747      8.00
     N    1723      7.00
     C    6290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 986 " - pdb=" SG  CYS A1159 " 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: 2.68
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2532

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 7 sheets defined
      53.5% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 215 through 228
    Processing helix  chain 'A' and resid 231 through 239
      removed outlier: 3.794A  pdb=" N   THR A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 253
      removed outlier: 3.505A  pdb=" N   PHE A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 280
      removed outlier: 3.674A  pdb=" N   ILE A 260 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 311
      removed outlier: 3.757A  pdb=" N   TYR A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 348
    Processing helix  chain 'A' and resid 359 through 372
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 3.952A  pdb=" N   ALA A 385 " --> pdb=" O   GLU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 439
      removed outlier: 3.678A  pdb=" N   GLN A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 457
      removed outlier: 3.791A  pdb=" N   CYS A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
      removed outlier: 3.647A  pdb=" N   LEU A 472 " --> pdb=" O   TYR A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 487
    Processing helix  chain 'A' and resid 497 through 506
    Processing helix  chain 'A' and resid 507 through 530
      removed outlier: 4.629A  pdb=" N   TRP A 513 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LYS A 529 " --> pdb=" O   SER A 525 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN A 530 " --> pdb=" O   ALA A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 608
      removed outlier: 3.682A  pdb=" N   THR A 604 " --> pdb=" O   LEU A 600 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ASN A 605 " --> pdb=" O   SER A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 624
    Processing helix  chain 'A' and resid 630 through 637
    Processing helix  chain 'A' and resid 640 through 659
    Processing helix  chain 'A' and resid 661 through 677
      removed outlier: 3.527A  pdb=" N   GLU A 665 " --> pdb=" O   LYS A 661 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG A 672 " --> pdb=" O   GLN A 668 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   TYR A 673 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 680
      No H-bonds generated for 'chain 'A' and resid 678 through 680'
    Processing helix  chain 'A' and resid 687 through 695
      removed outlier: 3.501A  pdb=" N   SER A 693 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE A 695 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 721
    Processing helix  chain 'A' and resid 748 through 756
      removed outlier: 3.682A  pdb=" N   LEU A 752 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   CYS A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 785
      removed outlier: 4.081A  pdb=" N   LYS A 779 " --> pdb=" O   GLY A 775 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ILE A 780 " --> pdb=" O   MET A 776 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 781 " --> pdb=" O   TYR A 777 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A 783 " --> pdb=" O   LYS A 779 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   HIS A 785 " --> pdb=" O   ILE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 828
    Processing helix  chain 'A' and resid 830 through 846
      removed outlier: 3.692A  pdb=" N   ILE A 839 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 852
      removed outlier: 3.569A  pdb=" N   LEU A 851 " --> pdb=" O   THR A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 871
    Processing helix  chain 'A' and resid 880 through 889
    Processing helix  chain 'A' and resid 894 through 910
      removed outlier: 4.736A  pdb=" N   ASP A 901 " --> pdb=" O   GLN A 897 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG A 904 " --> pdb=" O   GLU A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 952
    Processing helix  chain 'A' and resid 960 through 979
      removed outlier: 3.700A  pdb=" N   LYS A 964 " --> pdb=" O   ASN A 960 " (cutoff:3.500A)
      Proline residue:  A 968  - end of helix
      removed outlier: 4.540A  pdb=" N   GLY A 972 " --> pdb=" O   PRO A 968 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1012
      removed outlier: 3.573A  pdb=" N   PHE A1011 " --> pdb=" O   MET A1007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1015
      No H-bonds generated for 'chain 'A' and resid 1013 through 1015'
    Processing helix  chain 'A' and resid 1016 through 1029
      removed outlier: 4.088A  pdb=" N   ARG A1029 " --> pdb=" O   SER A1025 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1044
      removed outlier: 3.825A  pdb=" N   GLY A1044 " --> pdb=" O   LYS A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1063
    Processing helix  chain 'A' and resid 1089 through 1116
      removed outlier: 3.793A  pdb=" N   SER A1106 " --> pdb=" O   GLU A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1121
      removed outlier: 4.239A  pdb=" N   SER A1121 " --> pdb=" O   PRO A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1147 through 1164
      removed outlier: 3.805A  pdb=" N   LYS A1163 " --> pdb=" O   CYS A1159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1202 through 1207
    Processing helix  chain 'A' and resid 1219 through 1235
    Processing helix  chain 'A' and resid 1238 through 1257
    Processing helix  chain 'A' and resid 1263 through 1275
      removed outlier: 3.829A  pdb=" N   GLU A1267 " --> pdb=" O   GLU A1263 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LYS A1270 " --> pdb=" O   LEU A1266 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A1271 " --> pdb=" O   GLU A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1281
    Processing helix  chain 'A' and resid 1295 through 1307
    Processing helix  chain 'A' and resid 1308 through 1316
    Processing helix  chain 'A' and resid 1358 through 1368
    Processing helix  chain 'A' and resid 1374 through 1380
      removed outlier: 4.159A  pdb=" N   ILE A1378 " --> pdb=" O   TRP A1374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1381 through 1384
    Processing helix  chain 'A' and resid 1391 through 1404
    Processing helix  chain 'A' and resid 1409 through 1414
    Processing helix  chain 'A' and resid 1416 through 1427
      removed outlier: 3.520A  pdb=" N   LYS A1420 " --> pdb=" O   ASN A1416 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A1425 " --> pdb=" O   VAL A1421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1449 through 1457
    Processing helix  chain 'A' and resid 1459 through 1469
      removed outlier: 4.531A  pdb=" N   GLU A1469 " --> pdb=" O   PHE A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1492 through 1496
      removed outlier: 3.607A  pdb=" N   ILE A1496 " --> pdb=" O   LYS A1493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1510
    Processing helix  chain 'A' and resid 1518 through 1530
      Proline residue:  A1525  - end of helix
      removed outlier: 3.888A  pdb=" N   LEU A1528 " --> pdb=" O   SER A1524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1550 through 1559
    Processing helix  chain 'A' and resid 1574 through 1582
    Processing helix  chain 'A' and resid 1976 through 1989
      removed outlier: 4.110A  pdb=" N   SER A1980 " --> pdb=" O   ASN A1976 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 416 through 418
      removed outlier: 4.230A  pdb=" N   ALA A 416 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE A 537 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 418
      removed outlier: 4.230A  pdb=" N   ALA A 416 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE A 537 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 724 through 727
    Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 857
    Processing sheet with id=AA5, first strand: chain 'A' and resid 928 through 931
      removed outlier: 7.293A  pdb=" N   ILE A 914 " --> pdb=" O   MET A1033 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1192 through 1194
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1490 through 1491

    509 hydrogen bonds defined for protein.
    1464 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: 3.37

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3136
        1.34 -     1.47: 2541
        1.47 -     1.60: 4265
        1.60 -     1.73: 1
        1.73 -     1.86: 95
  Bond restraints: 10038
  Sorted by residual:
  bond pdb=" CB  PHE A 495 "
       pdb=" CG  PHE A 495 "
    ideal  model  delta    sigma   weight residual
    1.502  1.600 -0.098 2.30e-02 1.89e+03 1.80e+01
  bond pdb=" N   GLU A1165 "
       pdb=" CA  GLU A1165 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.15e-02 7.56e+03 1.50e+01
  bond pdb=" CA  PHE A 495 "
       pdb=" CB  PHE A 495 "
    ideal  model  delta    sigma   weight residual
    1.527  1.571 -0.044 1.44e-02 4.82e+03 9.32e+00
  bond pdb=" N   VAL A1421 "
       pdb=" CA  VAL A1421 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.16e+00
  bond pdb=" C   GLY A 494 "
       pdb=" N   PHE A 495 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 1.26e-02 6.30e+03 8.76e+00
  ... (remaining 10033 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 13076
        2.52 -     5.04: 441
        5.04 -     7.57: 62
        7.57 -    10.09: 12
       10.09 -    12.61: 3
  Bond angle restraints: 13594
  Sorted by residual:
  angle pdb=" N   PHE A 495 "
        pdb=" CA  PHE A 495 "
        pdb=" C   PHE A 495 "
      ideal   model   delta    sigma   weight residual
     110.19  101.16    9.03 1.24e+00 6.50e-01 5.31e+01
  angle pdb=" CA  PHE A 495 "
        pdb=" C   PHE A 495 "
        pdb=" N   ASN A 496 "
      ideal   model   delta    sigma   weight residual
     115.58  126.50  -10.92 1.55e+00 4.16e-01 4.96e+01
  angle pdb=" CA  PHE A 495 "
        pdb=" C   PHE A 495 "
        pdb=" O   PHE A 495 "
      ideal   model   delta    sigma   weight residual
     122.01  116.20    5.81 1.05e+00 9.07e-01 3.06e+01
  angle pdb=" N   SER A 323 "
        pdb=" CA  SER A 323 "
        pdb=" C   SER A 323 "
      ideal   model   delta    sigma   weight residual
     110.35  118.09   -7.74 1.40e+00 5.10e-01 3.06e+01
  angle pdb=" C   SER A 322 "
        pdb=" N   SER A 323 "
        pdb=" CA  SER A 323 "
      ideal   model   delta    sigma   weight residual
     121.31  129.15   -7.84 1.49e+00 4.50e-01 2.77e+01
  ... (remaining 13589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.67: 5620
       22.67 -    45.35: 240
       45.35 -    68.02: 43
       68.02 -    90.70: 7
       90.70 -   113.37: 2
  Dihedral angle restraints: 5912
    sinusoidal: 1949
      harmonic: 3963
  Sorted by residual:
  dihedral pdb=" CA  ASP A 574 "
           pdb=" C   ASP A 574 "
           pdb=" N   LEU A 575 "
           pdb=" CA  LEU A 575 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.42   56.58     0      5.00e+00 4.00e-02 1.28e+02
  dihedral pdb=" CA  SER A 322 "
           pdb=" C   SER A 322 "
           pdb=" N   SER A 323 "
           pdb=" CA  SER A 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -126.77  -53.23     0      5.00e+00 4.00e-02 1.13e+02
  dihedral pdb=" CB  CYS A 986 "
           pdb=" SG  CYS A 986 "
           pdb=" SG  CYS A1159 "
           pdb=" CB  CYS A1159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.07   74.07     1      1.00e+01 1.00e-02 6.96e+01
  ... (remaining 5909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1203
       0.065 -    0.129: 265
       0.129 -    0.194: 48
       0.194 -    0.259: 6
       0.259 -    0.323: 3
  Chirality restraints: 1525
  Sorted by residual:
  chirality pdb=" CB  ILE A 781 "
            pdb=" CA  ILE A 781 "
            pdb=" CG1 ILE A 781 "
            pdb=" CG2 ILE A 781 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  PHE A 495 "
            pdb=" N   PHE A 495 "
            pdb=" C   PHE A 495 "
            pdb=" CB  PHE A 495 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ILE A 325 "
            pdb=" N   ILE A 325 "
            pdb=" C   ILE A 325 "
            pdb=" CB  ILE A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 1522 not shown)

  Planarity restraints: 1748
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 573 "   -0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   PHE A 573 "    0.055 2.00e-02 2.50e+03
        pdb=" O   PHE A 573 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASP A 574 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1563 "   -0.046 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO A1564 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A1564 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A1564 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 495 "   -0.015 2.00e-02 2.50e+03   2.76e-02 7.62e+00
        pdb=" C   PHE A 495 "    0.048 2.00e-02 2.50e+03
        pdb=" O   PHE A 495 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A 496 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1745 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 46
        2.56 -     3.15: 8266
        3.15 -     3.73: 15368
        3.73 -     4.32: 20314
        4.32 -     4.90: 33823
  Nonbonded interactions: 77817
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 960 "
            pdb=" OD1 ASN A 960 "
     model   vdw
     1.975 3.040
  nonbonded pdb=" NE2 GLN A 483 "
            pdb=" CD1 PHE A 495 "
     model   vdw
     1.992 3.420
  nonbonded pdb=" NE2 GLN A 483 "
            pdb=" CE1 PHE A 495 "
     model   vdw
     2.169 3.420
  nonbonded pdb=" O   ALA A 792 "
            pdb=" N   LYS A 797 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" NZ  LYS A 339 "
            pdb=" O   VAL A1261 "
     model   vdw
     2.237 3.120
  ... (remaining 77812 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:             0.310
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.940
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
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   0.098  10038  Z= 0.422
  Angle     :  1.090  12.610  13594  Z= 0.627
  Chirality :  0.057   0.323   1525
  Planarity :  0.007   0.070   1748
  Dihedral  : 13.713 113.372   3377
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    Twisted General : 0.22 %

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: -1.90 (0.20), residues: 1396
  helix: -0.33 (0.19), residues: 653
  sheet: -2.60 (0.53), residues: 65
  loop : -2.08 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1275 
 HIS   0.011   0.002   HIS A 913 
 PHE   0.045   0.003   PHE A 495 
 TYR   0.020   0.003   TYR A1169 
 ARG   0.004   0.001   ARG A 316 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A 602 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  248 ASP cc_start: 0.8281 (m-30) cc_final: 0.8063 (m-30)
REVERT: A  700 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7403 (mmm160)
REVERT: A  727 LYS cc_start: 0.5501 (tttt) cc_final: 0.5108 (mttt)
REVERT: A  757 TYR cc_start: 0.8378 (m-80) cc_final: 0.7942 (m-80)
REVERT: A 1059 PHE cc_start: 0.8636 (t80) cc_final: 0.8432 (t80)
REVERT: A 1107 LEU cc_start: 0.9126 (tp) cc_final: 0.8898 (tt)
REVERT: A 1187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: A 1580 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6657 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.2082
  time to fit residues: 75.2913
Evaluate side-chains
  183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 106 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0060
   chunk 71 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
A 785 HIS
A1100 HIS
A1197 GLN
A1287 ASN
A1381 ASN
A1479 ASN
A1570 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.098116 restraints weight = 20042.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101068 restraints weight = 10083.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.103007 restraints weight = 6428.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10038  Z= 0.195
  Angle     :  0.615   8.559  13594  Z= 0.322
  Chirality :  0.042   0.157   1525
  Planarity :  0.005   0.056   1748
  Dihedral  :  4.956  34.549   1473
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.97 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.82 (0.22), residues: 1396
  helix:  0.75 (0.20), residues: 674
  sheet: -1.79 (0.58), residues: 65
  loop : -1.85 (0.23), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1017 
 HIS   0.020   0.002   HIS A1063 
 PHE   0.014   0.002   PHE A1239 
 TYR   0.019   0.002   TYR A1313 
 ARG   0.005   0.000   ARG A1029 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A 918 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  258 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: A  262 ARG cc_start: 0.8690 (ttp-170) cc_final: 0.8438 (ttp-170)
REVERT: A  505 PHE cc_start: 0.8259 (m-80) cc_final: 0.8047 (t80)
REVERT: A  727 LYS cc_start: 0.5717 (tttt) cc_final: 0.5308 (mtpt)
REVERT: A  929 TYR cc_start: 0.8080 (m-80) cc_final: 0.7858 (m-80)
  outliers start: 21
  outliers final: 11
  residues processed: 205
  average time/residue: 0.1929
  time to fit residues: 58.7517
Evaluate side-chains
  181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  785 HIS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1304 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 132 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 114 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
A 439 GLN
** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1276 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.098024 restraints weight = 20282.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101059 restraints weight = 10156.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103027 restraints weight = 6446.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10038  Z= 0.175
  Angle     :  0.568   8.143  13594  Z= 0.298
  Chirality :  0.041   0.154   1525
  Planarity :  0.005   0.055   1748
  Dihedral  :  4.709  39.197   1473
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.42 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.43 (0.22), residues: 1396
  helix:  1.16 (0.20), residues: 675
  sheet: -1.15 (0.63), residues: 65
  loop : -1.81 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1559 
 HIS   0.011   0.001   HIS A1063 
 PHE   0.016   0.001   PHE A1059 
 TYR   0.017   0.001   TYR A 867 
 ARG   0.007   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  258 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: A  727 LYS cc_start: 0.5846 (tttt) cc_final: 0.5483 (mttt)
REVERT: A  929 TYR cc_start: 0.8149 (m-80) cc_final: 0.7917 (m-80)
  outliers start: 24
  outliers final: 13
  residues processed: 193
  average time/residue: 0.1783
  time to fit residues: 51.7229
Evaluate side-chains
  178 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 116 optimal weight:    4.9990
   chunk 137 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 130 optimal weight:    0.3980
   chunk 108 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 785 HIS
A1276 ASN
A1570 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.119668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.097616 restraints weight = 20104.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.100661 restraints weight = 10056.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.102633 restraints weight = 6410.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10038  Z= 0.168
  Angle     :  0.536   7.021  13594  Z= 0.281
  Chirality :  0.040   0.143   1525
  Planarity :  0.005   0.057   1748
  Dihedral  :  4.380  35.225   1473
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.88 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.17 (0.23), residues: 1396
  helix:  1.37 (0.20), residues: 678
  sheet: -0.63 (0.65), residues: 65
  loop : -1.74 (0.23), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1559 
 HIS   0.006   0.001   HIS A1253 
 PHE   0.011   0.001   PHE A1546 
 TYR   0.027   0.001   TYR A 867 
 ARG   0.005   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 174
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  258 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8438 (tm-30)
REVERT: A  727 LYS cc_start: 0.5865 (tttt) cc_final: 0.5526 (mttt)
REVERT: A  929 TYR cc_start: 0.8138 (m-80) cc_final: 0.7907 (m-80)
  outliers start: 25
  outliers final: 18
  residues processed: 189
  average time/residue: 0.1760
  time to fit residues: 50.5490
Evaluate side-chains
  184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  785 HIS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue  943 GLU
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 805 HIS
A1189 ASN
A1247 GLN
** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 ASN
A1503 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.091844 restraints weight = 20170.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094755 restraints weight = 10177.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096683 restraints weight = 6516.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10038  Z= 0.317
  Angle     :  0.600   6.812  13594  Z= 0.319
  Chirality :  0.043   0.143   1525
  Planarity :  0.005   0.057   1748
  Dihedral  :  4.738  41.345   1473
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.48 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.17 (0.23), residues: 1396
  helix:  1.36 (0.20), residues: 669
  sheet: -0.69 (0.65), residues: 65
  loop : -1.67 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1559 
 HIS   0.006   0.001   HIS A1253 
 PHE   0.018   0.002   PHE A 247 
 TYR   0.017   0.002   TYR A 867 
 ARG   0.005   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 1.034 
Fit side-chains
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  727 LYS cc_start: 0.6161 (tttt) cc_final: 0.5754 (mtpt)
REVERT: A  804 MET cc_start: 0.8893 (tpp) cc_final: 0.8622 (tpp)
REVERT: A  929 TYR cc_start: 0.8399 (m-80) cc_final: 0.7996 (m-80)
REVERT: A 1307 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8011 (p)
  outliers start: 33
  outliers final: 21
  residues processed: 186
  average time/residue: 0.1713
  time to fit residues: 48.8540
Evaluate side-chains
  180 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1276 ASN
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 111 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 98 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0070
   chunk 79 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   overall best weight:    1.5602

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

Flipped N/Q/H residues before XYZ refinement:
A1276 ASN
A1381 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094349 restraints weight = 20447.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.097286 restraints weight = 10246.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.099206 restraints weight = 6583.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10038  Z= 0.203
  Angle     :  0.542   7.145  13594  Z= 0.286
  Chirality :  0.041   0.136   1525
  Planarity :  0.005   0.058   1748
  Dihedral  :  4.440  36.766   1473
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.70 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.05 (0.23), residues: 1396
  helix:  1.49 (0.20), residues: 674
  sheet: -0.65 (0.65), residues: 66
  loop : -1.68 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1559 
 HIS   0.012   0.001   HIS A 785 
 PHE   0.012   0.001   PHE A1546 
 TYR   0.017   0.001   TYR A 867 
 ARG   0.005   0.000   ARG A 262 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  368 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8904 (tt)
REVERT: A  727 LYS cc_start: 0.6307 (tttt) cc_final: 0.5892 (mtpt)
REVERT: A  804 MET cc_start: 0.8829 (tpp) cc_final: 0.8554 (tpp)
REVERT: A  929 TYR cc_start: 0.8224 (m-80) cc_final: 0.7917 (m-80)
REVERT: A  943 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8344 (mm-30)
REVERT: A 1307 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8008 (p)
REVERT: A 1580 ARG cc_start: 0.7114 (tpt170) cc_final: 0.6614 (tpp-160)
  outliers start: 29
  outliers final: 21
  residues processed: 185
  average time/residue: 0.1766
  time to fit residues: 49.4590
Evaluate side-chains
  185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue  943 GLU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1381 ASN
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 122 optimal weight:    0.0050
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 123 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 134 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    3.0002

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.113112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.091176 restraints weight = 20762.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.094086 restraints weight = 10441.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.095970 restraints weight = 6715.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10038  Z= 0.301
  Angle     :  0.592   7.972  13594  Z= 0.312
  Chirality :  0.043   0.132   1525
  Planarity :  0.005   0.059   1748
  Dihedral  :  4.648  40.208   1473
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.82 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.14 (0.23), residues: 1396
  helix:  1.42 (0.20), residues: 677
  sheet: -0.76 (0.68), residues: 72
  loop : -1.73 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1328 
 HIS   0.008   0.001   HIS A 785 
 PHE   0.014   0.002   PHE A 247 
 TYR   0.019   0.002   TYR A1169 
 ARG   0.006   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  368 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8893 (tt)
REVERT: A  727 LYS cc_start: 0.6413 (tttt) cc_final: 0.6014 (mttt)
REVERT: A  929 TYR cc_start: 0.8324 (m-80) cc_final: 0.7895 (m-80)
REVERT: A 1013 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8123 (m)
REVERT: A 1307 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8130 (p)
  outliers start: 33
  outliers final: 23
  residues processed: 180
  average time/residue: 0.1783
  time to fit residues: 48.9082
Evaluate side-chains
  177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  756 CYS
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue  931 MET
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 110 optimal weight:   20.0000
   chunk 121 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0970
   chunk 52 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 134 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 131 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 136 optimal weight:   10.0000
   overall best weight:    1.2580

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.116317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094612 restraints weight = 20354.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.097604 restraints weight = 10065.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099541 restraints weight = 6377.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10038  Z= 0.189
  Angle     :  0.546   8.248  13594  Z= 0.287
  Chirality :  0.041   0.138   1525
  Planarity :  0.005   0.061   1748
  Dihedral  :  4.372  35.865   1473
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.42 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.00 (0.23), residues: 1396
  helix:  1.55 (0.20), residues: 676
  sheet: -0.57 (0.68), residues: 70
  loop : -1.70 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A1559 
 HIS   0.008   0.001   HIS A 785 
 PHE   0.014   0.001   PHE A1546 
 TYR   0.016   0.001   TYR A 867 
 ARG   0.005   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  462 TRP cc_start: 0.8068 (m100) cc_final: 0.7725 (m100)
REVERT: A  568 ARG cc_start: 0.8196 (tpt90) cc_final: 0.7866 (tpt90)
REVERT: A  727 LYS cc_start: 0.6410 (tttt) cc_final: 0.5976 (mtpt)
REVERT: A  929 TYR cc_start: 0.8176 (m-80) cc_final: 0.7841 (m-10)
REVERT: A 1307 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8009 (p)
REVERT: A 1580 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6630 (tpp-160)
REVERT: A 1967 MET cc_start: 0.7910 (ptp) cc_final: 0.7670 (ptt)
  outliers start: 28
  outliers final: 22
  residues processed: 183
  average time/residue: 0.1855
  time to fit residues: 51.8911
Evaluate side-chains
  182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  756 CYS
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1317 MET
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 119 optimal weight:   10.0000
   chunk 138 optimal weight:    9.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A1369 ASN
A1381 ASN
** A1503 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.111413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.089316 restraints weight = 20821.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092120 restraints weight = 10624.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.093952 restraints weight = 6905.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  10038  Z= 0.369
  Angle     :  0.645   9.605  13594  Z= 0.340
  Chirality :  0.044   0.136   1525
  Planarity :  0.005   0.062   1748
  Dihedral  :  4.870  42.674   1473
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.55 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.24 (0.23), residues: 1396
  helix:  1.35 (0.20), residues: 671
  sheet: -0.90 (0.65), residues: 73
  loop : -1.76 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1559 
 HIS   0.007   0.001   HIS A1253 
 PHE   0.019   0.002   PHE A 247 
 TYR   0.017   0.002   TYR A 413 
 ARG   0.006   0.001   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  727 LYS cc_start: 0.6627 (tttt) cc_final: 0.6214 (mtpt)
REVERT: A  900 GLU cc_start: 0.7766 (tp30) cc_final: 0.7226 (tp30)
REVERT: A 1013 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8087 (m)
REVERT: A 1307 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8142 (p)
REVERT: A 1967 MET cc_start: 0.8003 (ptp) cc_final: 0.7755 (ptt)
  outliers start: 30
  outliers final: 25
  residues processed: 167
  average time/residue: 0.1660
  time to fit residues: 42.5450
Evaluate side-chains
  171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  756 CYS
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1304 ILE
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1317 MET
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 135 optimal weight:    0.4980
   chunk 79 optimal weight:    0.8980
   chunk 121 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0970
   chunk 75 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0040
   chunk 16 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.116286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.094485 restraints weight = 20493.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.097362 restraints weight = 10294.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099280 restraints weight = 6628.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10038  Z= 0.177
  Angle     :  0.566  10.311  13594  Z= 0.293
  Chirality :  0.041   0.147   1525
  Planarity :  0.005   0.061   1748
  Dihedral  :  4.401  35.551   1473
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.15 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.01 (0.23), residues: 1396
  helix:  1.57 (0.20), residues: 670
  sheet: -0.39 (0.68), residues: 72
  loop : -1.70 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1559 
 HIS   0.007   0.001   HIS A1253 
 PHE   0.015   0.001   PHE A1546 
 TYR   0.013   0.001   TYR A 867 
 ARG   0.005   0.000   ARG A 850 

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

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

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2792 Ramachandran restraints generated.
    1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it.
REVERT: A  462 TRP cc_start: 0.8027 (m100) cc_final: 0.7685 (m100)
REVERT: A  568 ARG cc_start: 0.8178 (tpt90) cc_final: 0.7874 (tpt90)
REVERT: A  727 LYS cc_start: 0.6416 (tttt) cc_final: 0.6095 (mttt)
REVERT: A  900 GLU cc_start: 0.7580 (tp30) cc_final: 0.7143 (tp30)
REVERT: A  929 TYR cc_start: 0.8123 (m-10) cc_final: 0.7788 (m-10)
REVERT: A 1307 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8006 (p)
REVERT: A 1580 ARG cc_start: 0.7066 (tpt170) cc_final: 0.6717 (tpp-160)
REVERT: A 1967 MET cc_start: 0.7896 (ptp) cc_final: 0.7674 (ptt)
  outliers start: 27
  outliers final: 24
  residues processed: 178
  average time/residue: 0.1854
  time to fit residues: 49.9940
Evaluate side-chains
  182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  756 CYS
Chi-restraints excluded: chain A residue  780 ILE
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  901 ASP
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1063 HIS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1250 CYS
Chi-restraints excluded: chain A residue 1256 LEU
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1304 ILE
Chi-restraints excluded: chain A residue 1307 THR
Chi-restraints excluded: chain A residue 1317 MET
Chi-restraints excluded: chain A residue 1453 LEU
Chi-restraints excluded: chain A residue 1521 LEU
Chi-restraints excluded: chain A residue 1563 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 137 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 111 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 113 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS
A1479 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.117076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.095688 restraints weight = 20240.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098562 restraints weight = 10325.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100422 restraints weight = 6649.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10038  Z= 0.171
  Angle     :  0.555  10.629  13594  Z= 0.285
  Chirality :  0.040   0.147   1525
  Planarity :  0.005   0.062   1748
  Dihedral  :  4.232  33.866   1473
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.39 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.10 (0.23), residues: 1396
  helix:  1.66 (0.20), residues: 677
  sheet: -0.30 (0.68), residues: 72
  loop : -1.73 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1328 
 HIS   0.014   0.001   HIS A1253 
 PHE   0.022   0.001   PHE A1301 
 TYR   0.017   0.001   TYR A 867 
 ARG   0.003   0.000   ARG A 850 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2795.34 seconds
wall clock time: 49 minutes 26.46 seconds (2966.46 seconds total)