Starting phenix.real_space_refine
on Mon Jun  9 00:47:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wli_32584/06_2025/7wli_32584_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.068
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       1      5.49       5
     S      78      5.16       5
     C    6321      2.51       5
     N    1501      2.21       5
     O    1590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9493
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9111
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 24
      Conformer: "B"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 24
          bond proxies already assigned to first conformer: 9289
    Chain: "A"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 382
          Unusual residues: {' CA': 2, '3PE': 11, 'NAG': 2, 'Y01': 6}
          Classifications: {'undetermined': 21}
          Link IDs: {None: 20}
          Unresolved non-hydrogen bonds: 421
          Unresolved non-hydrogen angles: 487
          Unresolved non-hydrogen dihedrals: 433
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'Y01:plan-2': 1, '3PE:plan-1': 10, '3PE:plan-2': 10, 'Y01:plan-1': 3}
          Unresolved non-hydrogen planarities: 78
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 854 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 854 " occ=0.50
  Time building chain proxies: 9.59, per 1000 atoms: 1.01
  Number of scatterers: 9493
  At special positions: 0
  Unit cell: (112.32, 123.76, 109.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      2     19.99
     S      78     16.00
     P       1     15.00
     O    1590      8.00
     N    1501      7.00
     C    6321      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 239 " - pdb=" SG  CYS A 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 269 " - pdb=" SG  CYS A 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1335 " - pdb=" SG  CYS A1349 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1646 " - pdb=" SG  CYS A1652 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1691 " - pdb=" SG  CYS A1698 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A2303 " - " ASN A1345 "
      " NAG A2304 " - " ASN A1342 "
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2150

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      76.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 78
      removed outlier: 4.192A  pdb=" N   CYS A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   LYS A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   MET A  75 " --> pdb=" O   TRP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 98
      removed outlier: 3.796A  pdb=" N   GLU A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 138
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 170
      removed outlier: 3.586A  pdb=" N   ARG A 152 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 4.313A  pdb=" N   VAL A 182 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      Proline residue:  A 185  - end of helix
    Processing helix  chain 'A' and resid 192 through 206
    Processing helix  chain 'A' and resid 209 through 231
      removed outlier: 4.308A  pdb=" N   PHE A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 260 through 264
      removed outlier: 3.561A  pdb=" N   ASP A 263 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 355
      removed outlier: 3.779A  pdb=" N   ALA A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 370
      removed outlier: 3.586A  pdb=" N   ILE A 362 " --> pdb=" O   GLY A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 373
      No H-bonds generated for 'chain 'A' and resid 371 through 373'
    Processing helix  chain 'A' and resid 374 through 383
    Processing helix  chain 'A' and resid 389 through 413
      removed outlier: 3.742A  pdb=" N   MET A 412 " --> pdb=" O   GLU A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 638
      removed outlier: 4.111A  pdb=" N   LYS A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL A 637 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 660
      removed outlier: 4.200A  pdb=" N   GLU A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 695
      removed outlier: 3.768A  pdb=" N   ASN A 670 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 3.895A  pdb=" N   ASN A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 721
      removed outlier: 3.662A  pdb=" N   ILE A 706 " --> pdb=" O   ASN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 731 through 744
      removed outlier: 3.861A  pdb=" N   LEU A 735 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 785
      removed outlier: 3.643A  pdb=" N   ARG A 750 " --> pdb=" O   PRO A 746 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A 752 " --> pdb=" O   LEU A 748 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ASN A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   THR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE A 765 " --> pdb=" O   ASN A 761 " (cutoff:3.500A)
WARNING: missing atoms!
    Processing helix  chain 'A' and resid 806 through 820
    Processing helix  chain 'A' and resid 822 through 832
      removed outlier: 3.599A  pdb=" N   VAL A 826 " --> pdb=" O   ASP A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 837
      No H-bonds generated for 'chain 'A' and resid 835 through 837'
    Processing helix  chain 'A' and resid 838 through 850
      removed outlier: 3.990A  pdb=" N   PHE A 842 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 866
    Processing helix  chain 'A' and resid 1171 through 1188
    Processing helix  chain 'A' and resid 1198 through 1227
    Processing helix  chain 'A' and resid 1234 through 1237
      removed outlier: 3.520A  pdb=" N   ARG A1237 " --> pdb=" O   ALA A1234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1234 through 1237'
    Processing helix  chain 'A' and resid 1238 through 1260
    Processing helix  chain 'A' and resid 1267 through 1281
    Processing helix  chain 'A' and resid 1289 through 1302
    Processing helix  chain 'A' and resid 1306 through 1328
    Processing helix  chain 'A' and resid 1345 through 1353
    Processing helix  chain 'A' and resid 1365 through 1378
    Processing helix  chain 'A' and resid 1381 through 1392
      removed outlier: 3.695A  pdb=" N   ILE A1385 " --> pdb=" O   GLY A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1404 through 1406
      No H-bonds generated for 'chain 'A' and resid 1404 through 1406'
    Processing helix  chain 'A' and resid 1407 through 1463
      removed outlier: 3.918A  pdb=" N   LEU A1415 " --> pdb=" O   PHE A1411 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A1436 " --> pdb=" O   GLU A1432 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLU A1451 " --> pdb=" O   ARG A1447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1505
      removed outlier: 3.564A  pdb=" N   ASP A1490 " --> pdb=" O   SER A1486 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   PHE A1492 " --> pdb=" O   TYR A1488 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE A1493 " --> pdb=" O   LEU A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1541
    Processing helix  chain 'A' and resid 1542 through 1549
      removed outlier: 3.575A  pdb=" N   PHE A1546 " --> pdb=" O   GLY A1542 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A1547 " --> pdb=" O   LEU A1543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1551 through 1575
      removed outlier: 3.577A  pdb=" N   LEU A1568 " --> pdb=" O   MET A1564 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU A1569 " --> pdb=" O   GLY A1565 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A1570 " --> pdb=" O   ILE A1566 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE A1571 " --> pdb=" O   THR A1567 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A1572 " --> pdb=" O   LEU A1568 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A1573 " --> pdb=" O   GLU A1569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1580 through 1590
      removed outlier: 3.528A  pdb=" N   ILE A1584 " --> pdb=" O   ASN A1580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1600
      removed outlier: 3.660A  pdb=" N   LYS A1597 " --> pdb=" O   ARG A1594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1602 through 1614
    Processing helix  chain 'A' and resid 1615 through 1642
    Processing helix  chain 'A' and resid 1664 through 1676
      removed outlier: 3.863A  pdb=" N   THR A1670 " --> pdb=" O   MET A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1688
    Processing helix  chain 'A' and resid 1695 through 1700
      removed outlier: 4.173A  pdb=" N   LEU A1699 " --> pdb=" O   GLU A1695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1738
      removed outlier: 3.576A  pdb=" N   VAL A1705 " --> pdb=" O   SER A1701 " (cutoff:3.500A)
      Proline residue:  A1707  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 256 through 257
      removed outlier: 4.753A  pdb=" N   CYS A 239 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ARG A 238 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1333 through 1334

    616 hydrogen bonds defined for protein.
    1755 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: 3.02

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1426
        1.31 -     1.44: 2571
        1.44 -     1.57: 5441
        1.57 -     1.69: 137
        1.69 -     1.82: 127
  Bond restraints: 9702
  Sorted by residual:
  bond pdb=" C   ALA A1443 "
       pdb=" O   ALA A1443 "
    ideal  model  delta    sigma   weight residual
    1.236  1.356 -0.120 1.15e-02 7.56e+03 1.08e+02
  bond pdb=" C   GLN A1439 "
       pdb=" O   GLN A1439 "
    ideal  model  delta    sigma   weight residual
    1.236  1.328 -0.092 1.15e-02 7.56e+03 6.37e+01
  bond pdb=" C   LYS A1459 "
       pdb=" O   LYS A1459 "
    ideal  model  delta    sigma   weight residual
    1.237  1.330 -0.093 1.17e-02 7.31e+03 6.35e+01
  bond pdb=" C21 3PE A2305 "
       pdb=" O21 3PE A2305 "
    ideal  model  delta    sigma   weight residual
    1.316  1.468 -0.152 2.00e-02 2.50e+03 5.79e+01
  bond pdb=" C   GLU A1450 "
       pdb=" O   GLU A1450 "
    ideal  model  delta    sigma   weight residual
    1.237  1.316 -0.079 1.16e-02 7.43e+03 4.66e+01
  ... (remaining 9697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 12756
        2.98 -     5.95: 328
        5.95 -     8.93: 37
        8.93 -    11.90: 6
       11.90 -    14.88: 3
  Bond angle restraints: 13130
  Sorted by residual:
  angle pdb=" N   ALA A1443 "
        pdb=" CA  ALA A1443 "
        pdb=" C   ALA A1443 "
      ideal   model   delta    sigma   weight residual
     110.97  123.96  -12.99 1.09e+00 8.42e-01 1.42e+02
  angle pdb=" N   LYS A1463 "
        pdb=" CA  LYS A1463 "
        pdb=" C   LYS A1463 "
      ideal   model   delta    sigma   weight residual
     108.31  123.19  -14.88 1.52e+00 4.33e-01 9.58e+01
  angle pdb=" C   ALA A1446 "
        pdb=" N   ARG A1447 "
        pdb=" CA  ARG A1447 "
      ideal   model   delta    sigma   weight residual
     120.28  109.12   11.16 1.44e+00 4.82e-01 6.00e+01
  angle pdb=" N   ALA A1446 "
        pdb=" CA  ALA A1446 "
        pdb=" C   ALA A1446 "
      ideal   model   delta    sigma   weight residual
     111.07  103.08    7.99 1.07e+00 8.73e-01 5.57e+01
  angle pdb=" N   ARG A1453 "
        pdb=" CA  ARG A1453 "
        pdb=" C   ARG A1453 "
      ideal   model   delta    sigma   weight residual
     112.23  103.94    8.29 1.26e+00 6.30e-01 4.33e+01
  ... (remaining 13125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.12: 5328
       18.12 -    36.25: 606
       36.25 -    54.37: 132
       54.37 -    72.49: 21
       72.49 -    90.61: 5
  Dihedral angle restraints: 6092
    sinusoidal: 2773
      harmonic: 3319
  Sorted by residual:
  dihedral pdb=" CB  CYS A1646 "
           pdb=" SG  CYS A1646 "
           pdb=" SG  CYS A1652 "
           pdb=" CB  CYS A1652 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.76  -81.76     1      1.00e+01 1.00e-02 8.22e+01
  dihedral pdb=" CB  CYS A 239 "
           pdb=" SG  CYS A 239 "
           pdb=" SG  CYS A 280 "
           pdb=" CB  CYS A 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.97  -52.97     1      1.00e+01 1.00e-02 3.82e+01
  dihedral pdb=" CA  ASN A 332 "
           pdb=" C   ASN A 332 "
           pdb=" N   PRO A 333 "
           pdb=" CA  PRO A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.66  -28.34     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 6089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1444
       0.101 -    0.202: 64
       0.202 -    0.303: 15
       0.303 -    0.404: 6
       0.404 -    0.505: 6
  Chirality restraints: 1535
  Sorted by residual:
  chirality pdb=" CBG Y01 A2312 "
            pdb=" CAQ Y01 A2312 "
            pdb=" CBD Y01 A2312 "
            pdb=" CBI Y01 A2312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.84    0.51 2.00e-01 2.50e+01 6.39e+00
  chirality pdb=" CBG Y01 A2315 "
            pdb=" CAQ Y01 A2315 "
            pdb=" CBD Y01 A2315 "
            pdb=" CBI Y01 A2315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.82    0.49 2.00e-01 2.50e+01 6.04e+00
  chirality pdb=" CBG Y01 A2309 "
            pdb=" CAQ Y01 A2309 "
            pdb=" CBD Y01 A2309 "
            pdb=" CBI Y01 A2309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.82    0.49 2.00e-01 2.50e+01 6.03e+00
  ... (remaining 1532 not shown)

  Planarity restraints: 1579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1449 "   -0.024 2.00e-02 2.50e+03   4.64e-02 2.16e+01
        pdb=" C   ARG A1449 "    0.080 2.00e-02 2.50e+03
        pdb=" O   ARG A1449 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   GLU A1450 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 702 "    0.054 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO A 703 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 703 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 703 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 403 "   -0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" CD  GLU A 403 "    0.056 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 403 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 403 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1576 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 47
        2.49 -     3.09: 7232
        3.09 -     3.70: 14554
        3.70 -     4.30: 21308
        4.30 -     4.90: 34299
  Nonbonded interactions: 77440
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A1441 "
            pdb=" OD2 ASP A1734 "
     model   vdw
     1.888 3.040
  nonbonded pdb=" OD1 ASP A1380 "
            pdb=" ND2 ASN A1681 "
     model   vdw
     2.139 3.120
  nonbonded pdb=" O   HIS A1481 "
            pdb=" OG1 THR A1485 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG  SER A 270 "
            pdb=" O   ASP A 274 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OH  TYR A1524 "
            pdb=" OE1 GLU A1569 "
     model   vdw
     2.151 3.040
  ... (remaining 77435 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     29.100
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
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      :  0.012   0.152   9709  Z= 0.611
  Angle     :  1.014  14.878  13146  Z= 0.526
  Chirality :  0.064   0.505   1535
  Planarity :  0.005   0.081   1577
  Dihedral  : 15.399  90.614   3927
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.28 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.26), residues: 1130
  helix:  0.53 (0.19), residues: 759
  sheet:  None (None), residues: 0
  loop : -1.36 (0.36), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 823 
 HIS   0.005   0.001   HIS A1358 
 PHE   0.043   0.002   PHE A1626 
 TYR   0.019   0.002   TYR A1361 
 ARG   0.004   0.000   ARG A 749 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00507 (    2)
  link_NAG-ASN         : angle       2.90621 (    6)
  hydrogen bonds       : bond        0.13566 (  616)
  hydrogen bonds       : angle       6.17206 ( 1755)
  SS BOND              : bond        0.00179 (    5)
  SS BOND              : angle       1.40360 (   10)
  covalent geometry    : bond        0.01155 ( 9702)
  covalent geometry    : angle       1.01237 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ASN cc_start: 0.8806 (t0) cc_final: 0.8558 (t0)
REVERT: A  146 LEU cc_start: 0.8135 (mt) cc_final: 0.7385 (tt)
REVERT: A  648 MET cc_start: 0.6592 (mmp) cc_final: 0.6069 (tpt)
REVERT: A 1219 MET cc_start: 0.8386 (tpt) cc_final: 0.8080 (tpt)
REVERT: A 1564 MET cc_start: 0.8205 (ttm) cc_final: 0.7944 (tmm)
REVERT: A 1650 ASN cc_start: 0.7501 (m110) cc_final: 0.7122 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1844
  time to fit residues: 59.3190
Evaluate side-chains
  189 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 ASN
A 653 ASN
A 761 ASN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 ASN
A1404 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.205546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146309 restraints weight = 16128.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 3.15
r_work: 0.3470 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9709  Z= 0.164
  Angle     :  0.687  11.796  13146  Z= 0.348
  Chirality :  0.043   0.241   1535
  Planarity :  0.005   0.055   1577
  Dihedral  :  9.737  58.242   1807
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.74 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1130
  helix:  0.89 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -1.63 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1551 
 HIS   0.003   0.001   HIS A1358 
 PHE   0.033   0.002   PHE A1626 
 TYR   0.016   0.002   TYR A1633 
 ARG   0.006   0.000   ARG A 731 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    2)
  link_NAG-ASN         : angle       2.47904 (    6)
  hydrogen bonds       : bond        0.04859 (  616)
  hydrogen bonds       : angle       5.10467 ( 1755)
  SS BOND              : bond        0.00172 (    5)
  SS BOND              : angle       1.15180 (   10)
  covalent geometry    : bond        0.00368 ( 9702)
  covalent geometry    : angle       0.68420 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 203
  time to evaluate  : 1.084 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   78 ASN cc_start: 0.8794 (t0) cc_final: 0.8557 (t0)
REVERT: A  134 MET cc_start: 0.8276 (mpp) cc_final: 0.7998 (mpp)
REVERT: A  146 LEU cc_start: 0.8009 (mt) cc_final: 0.7253 (tt)
REVERT: A  648 MET cc_start: 0.6699 (mmp) cc_final: 0.6042 (tpt)
REVERT: A  686 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8168 (mm-30)
REVERT: A 1172 PHE cc_start: 0.8090 (t80) cc_final: 0.7337 (t80)
REVERT: A 1174 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7407 (m-80)
REVERT: A 1218 GLU cc_start: 0.7928 (pp20) cc_final: 0.7098 (tm-30)
REVERT: A 1434 PHE cc_start: 0.8707 (t80) cc_final: 0.8365 (t80)
REVERT: A 1600 LYS cc_start: 0.8437 (tptt) cc_final: 0.7610 (tptp)
REVERT: A 1650 ASN cc_start: 0.7568 (m110) cc_final: 0.7182 (m-40)
REVERT: A 1655 MET cc_start: 0.8094 (mtm) cc_final: 0.7766 (mtp)
  outliers start: 10
  outliers final: 6
  residues processed: 207
  average time/residue: 0.1751
  time to fit residues: 53.8330
Evaluate side-chains
  191 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 184
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1601 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 866 GLN
A1398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.206828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.147356 restraints weight = 15742.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 3.09
r_work: 0.3505 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9709  Z= 0.148
  Angle     :  0.642  14.455  13146  Z= 0.322
  Chirality :  0.041   0.228   1535
  Planarity :  0.004   0.049   1577
  Dihedral  :  9.116  59.414   1807
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.33 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1130
  helix:  1.00 (0.19), residues: 779
  sheet:  None (None), residues: 0
  loop : -1.69 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1551 
 HIS   0.005   0.001   HIS A1358 
 PHE   0.035   0.002   PHE A 744 
 TYR   0.013   0.001   TYR A 828 
 ARG   0.006   0.000   ARG A 731 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00353 (    2)
  link_NAG-ASN         : angle       2.39041 (    6)
  hydrogen bonds       : bond        0.04408 (  616)
  hydrogen bonds       : angle       4.84080 ( 1755)
  SS BOND              : bond        0.00128 (    5)
  SS BOND              : angle       0.93042 (   10)
  covalent geometry    : bond        0.00329 ( 9702)
  covalent geometry    : angle       0.63984 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 1.058 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ASN cc_start: 0.8770 (t0) cc_final: 0.8546 (t0)
REVERT: A  134 MET cc_start: 0.8019 (mpp) cc_final: 0.7549 (mpp)
REVERT: A  146 LEU cc_start: 0.8027 (mt) cc_final: 0.7272 (tt)
REVERT: A  648 MET cc_start: 0.6634 (mmp) cc_final: 0.6010 (tpt)
REVERT: A  657 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8103 (ttm)
REVERT: A 1174 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7380 (m-80)
REVERT: A 1434 PHE cc_start: 0.8619 (t80) cc_final: 0.8348 (t80)
REVERT: A 1655 MET cc_start: 0.8048 (mtm) cc_final: 0.7524 (mtp)
REVERT: A 1730 MET cc_start: 0.7902 (mmm) cc_final: 0.7636 (mmm)
  outliers start: 15
  outliers final: 6
  residues processed: 208
  average time/residue: 0.1837
  time to fit residues: 57.0424
Evaluate side-chains
  200 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 192
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1295 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 75 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.208501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148175 restraints weight = 19833.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 3.28
r_work: 0.3521 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9709  Z= 0.153
  Angle     :  0.625  10.244  13146  Z= 0.315
  Chirality :  0.042   0.227   1535
  Planarity :  0.004   0.048   1577
  Dihedral  :  8.901  59.530   1807
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.02 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.26), residues: 1130
  helix:  1.08 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop : -1.74 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1551 
 HIS   0.005   0.001   HIS A1358 
 PHE   0.023   0.002   PHE A1626 
 TYR   0.013   0.001   TYR A1387 
 ARG   0.003   0.000   ARG A1447 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00372 (    2)
  link_NAG-ASN         : angle       2.23167 (    6)
  hydrogen bonds       : bond        0.04245 (  616)
  hydrogen bonds       : angle       4.72763 ( 1755)
  SS BOND              : bond        0.00133 (    5)
  SS BOND              : angle       0.86110 (   10)
  covalent geometry    : bond        0.00350 ( 9702)
  covalent geometry    : angle       0.62341 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 0.925 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.7802 (mmm) cc_final: 0.7438 (mmp)
REVERT: A  134 MET cc_start: 0.8109 (mpp) cc_final: 0.7754 (mpp)
REVERT: A  403 GLU cc_start: 0.7370 (tp30) cc_final: 0.7158 (tp30)
REVERT: A  648 MET cc_start: 0.6729 (mmp) cc_final: 0.6091 (tpt)
REVERT: A  657 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8200 (ttm)
REVERT: A 1174 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7377 (m-80)
REVERT: A 1187 ILE cc_start: 0.7893 (mt) cc_final: 0.7515 (mt)
REVERT: A 1434 PHE cc_start: 0.8570 (t80) cc_final: 0.8335 (t80)
REVERT: A 1504 MET cc_start: 0.8588 (mtm) cc_final: 0.8274 (mtp)
REVERT: A 1655 MET cc_start: 0.8062 (mtm) cc_final: 0.7551 (mtp)
  outliers start: 15
  outliers final: 10
  residues processed: 207
  average time/residue: 0.1768
  time to fit residues: 54.1532
Evaluate side-chains
  198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 107 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 112 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.208211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148734 restraints weight = 21983.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 3.33
r_work: 0.3520 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9709  Z= 0.157
  Angle     :  0.617   9.534  13146  Z= 0.315
  Chirality :  0.042   0.227   1535
  Planarity :  0.004   0.047   1577
  Dihedral  :  8.747  59.441   1807
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.71 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.44 (0.26), residues: 1130
  helix:  1.16 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop : -1.68 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1551 
 HIS   0.004   0.001   HIS A1358 
 PHE   0.022   0.002   PHE A1172 
 TYR   0.014   0.001   TYR A1387 
 ARG   0.006   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    2)
  link_NAG-ASN         : angle       2.22264 (    6)
  hydrogen bonds       : bond        0.04123 (  616)
  hydrogen bonds       : angle       4.69609 ( 1755)
  SS BOND              : bond        0.00129 (    5)
  SS BOND              : angle       0.81525 (   10)
  covalent geometry    : bond        0.00363 ( 9702)
  covalent geometry    : angle       0.61539 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  648 MET cc_start: 0.6622 (mmp) cc_final: 0.5988 (tpt)
REVERT: A  657 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8228 (ttm)
REVERT: A 1174 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7389 (m-80)
REVERT: A 1218 GLU cc_start: 0.7980 (pp20) cc_final: 0.6950 (tm-30)
REVERT: A 1434 PHE cc_start: 0.8639 (t80) cc_final: 0.8407 (t80)
REVERT: A 1504 MET cc_start: 0.8618 (mtm) cc_final: 0.8275 (mtp)
REVERT: A 1655 MET cc_start: 0.8064 (mtm) cc_final: 0.7561 (mtp)
  outliers start: 16
  outliers final: 12
  residues processed: 200
  average time/residue: 0.2154
  time to fit residues: 65.0837
Evaluate side-chains
  198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1525 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 70 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1193 GLN
A1663 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.209996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.158974 restraints weight = 25593.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 4.17
r_work: 0.3498 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9709  Z= 0.147
  Angle     :  0.631  15.398  13146  Z= 0.316
  Chirality :  0.042   0.221   1535
  Planarity :  0.004   0.048   1577
  Dihedral  :  8.538  59.967   1807
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.61 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1130
  helix:  1.20 (0.19), residues: 777
  sheet:  None (None), residues: 0
  loop : -1.63 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1551 
 HIS   0.004   0.001   HIS A1358 
 PHE   0.020   0.002   PHE A 125 
 TYR   0.016   0.001   TYR A1387 
 ARG   0.006   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00443 (    2)
  link_NAG-ASN         : angle       2.23457 (    6)
  hydrogen bonds       : bond        0.04041 (  616)
  hydrogen bonds       : angle       4.65872 ( 1755)
  SS BOND              : bond        0.00133 (    5)
  SS BOND              : angle       0.75923 (   10)
  covalent geometry    : bond        0.00336 ( 9702)
  covalent geometry    : angle       0.62929 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  648 MET cc_start: 0.6531 (mmp) cc_final: 0.5896 (tpt)
REVERT: A  657 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8267 (ttm)
REVERT: A  733 PHE cc_start: 0.7717 (m-80) cc_final: 0.7340 (m-80)
REVERT: A 1174 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7392 (m-80)
REVERT: A 1218 GLU cc_start: 0.8083 (pp20) cc_final: 0.7768 (pp20)
REVERT: A 1434 PHE cc_start: 0.8695 (t80) cc_final: 0.8389 (t80)
REVERT: A 1504 MET cc_start: 0.8620 (mtm) cc_final: 0.8258 (mtp)
REVERT: A 1655 MET cc_start: 0.8013 (mtm) cc_final: 0.7540 (mtp)
REVERT: A 1730 MET cc_start: 0.8028 (mmm) cc_final: 0.7036 (mmm)
  outliers start: 17
  outliers final: 11
  residues processed: 203
  average time/residue: 0.1815
  time to fit residues: 54.9092
Evaluate side-chains
  198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 185
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1525 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 90 optimal weight:    0.0270
   chunk 79 optimal weight:    0.0670
   chunk 60 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9980
   chunk 88 optimal weight:    8.9990
   overall best weight:    0.5776

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.210669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.154615 restraints weight = 26606.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 3.15
r_work: 0.3606 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9709  Z= 0.138
  Angle     :  0.641  13.424  13146  Z= 0.323
  Chirality :  0.041   0.221   1535
  Planarity :  0.004   0.048   1577
  Dihedral  :  8.324  59.271   1807
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.40 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1130
  helix:  1.24 (0.19), residues: 779
  sheet:  None (None), residues: 0
  loop : -1.67 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1551 
 HIS   0.004   0.001   HIS A1358 
 PHE   0.019   0.002   PHE A 125 
 TYR   0.016   0.001   TYR A1387 
 ARG   0.005   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00413 (    2)
  link_NAG-ASN         : angle       2.14285 (    6)
  hydrogen bonds       : bond        0.03998 (  616)
  hydrogen bonds       : angle       4.64903 ( 1755)
  SS BOND              : bond        0.00120 (    5)
  SS BOND              : angle       0.72340 (   10)
  covalent geometry    : bond        0.00309 ( 9702)
  covalent geometry    : angle       0.63944 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7088 (tmm)
REVERT: A  648 MET cc_start: 0.6593 (mmp) cc_final: 0.5934 (tpt)
REVERT: A  733 PHE cc_start: 0.7646 (m-80) cc_final: 0.7355 (m-80)
REVERT: A 1174 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7427 (m-80)
REVERT: A 1218 GLU cc_start: 0.8000 (pp20) cc_final: 0.7033 (tm-30)
REVERT: A 1504 MET cc_start: 0.8564 (mtm) cc_final: 0.8170 (mtp)
REVERT: A 1655 MET cc_start: 0.7911 (mtm) cc_final: 0.7464 (mtp)
REVERT: A 1686 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.7794 (m-30)
REVERT: A 1709 TYR cc_start: 0.8531 (t80) cc_final: 0.8268 (t80)
  outliers start: 20
  outliers final: 9
  residues processed: 201
  average time/residue: 0.1760
  time to fit residues: 54.0605
Evaluate side-chains
  190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1393 VAL
Chi-restraints excluded: chain A residue 1525 MET
Chi-restraints excluded: chain A residue 1686 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 100 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.211132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.151509 restraints weight = 21182.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 3.21
r_work: 0.3550 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9709  Z= 0.143
  Angle     :  0.651  17.044  13146  Z= 0.325
  Chirality :  0.042   0.295   1535
  Planarity :  0.004   0.047   1577
  Dihedral  :  8.204  58.588   1807
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.10 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1130
  helix:  1.27 (0.19), residues: 779
  sheet:  None (None), residues: 0
  loop : -1.66 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1551 
 HIS   0.003   0.001   HIS A1358 
 PHE   0.021   0.002   PHE A 125 
 TYR   0.017   0.001   TYR A1387 
 ARG   0.005   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    2)
  link_NAG-ASN         : angle       2.11368 (    6)
  hydrogen bonds       : bond        0.03997 (  616)
  hydrogen bonds       : angle       4.60477 ( 1755)
  SS BOND              : bond        0.00123 (    5)
  SS BOND              : angle       0.71917 (   10)
  covalent geometry    : bond        0.00324 ( 9702)
  covalent geometry    : angle       0.64946 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7260 (tmm)
REVERT: A  648 MET cc_start: 0.6628 (mmp) cc_final: 0.5977 (tpt)
REVERT: A  733 PHE cc_start: 0.7691 (m-80) cc_final: 0.7400 (m-80)
REVERT: A 1174 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7434 (m-80)
REVERT: A 1179 PHE cc_start: 0.8878 (m-80) cc_final: 0.8544 (m-80)
REVERT: A 1218 GLU cc_start: 0.7955 (pp20) cc_final: 0.7725 (pp20)
REVERT: A 1434 PHE cc_start: 0.8580 (t80) cc_final: 0.8023 (t80)
REVERT: A 1504 MET cc_start: 0.8622 (mtm) cc_final: 0.8211 (mtp)
REVERT: A 1655 MET cc_start: 0.7949 (mtm) cc_final: 0.7515 (mtp)
REVERT: A 1686 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.7981 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 193
  average time/residue: 0.1940
  time to fit residues: 56.4223
Evaluate side-chains
  191 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1393 VAL
Chi-restraints excluded: chain A residue 1525 MET
Chi-restraints excluded: chain A residue 1686 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 866 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.211077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.151623 restraints weight = 18983.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 3.04
r_work: 0.3580 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9709  Z= 0.145
  Angle     :  0.667  15.165  13146  Z= 0.335
  Chirality :  0.042   0.286   1535
  Planarity :  0.004   0.047   1577
  Dihedral  :  8.133  58.464   1807
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.59 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1130
  helix:  1.29 (0.19), residues: 781
  sheet:  None (None), residues: 0
  loop : -1.70 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1551 
 HIS   0.003   0.001   HIS A1358 
 PHE   0.041   0.002   PHE A 125 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    2)
  link_NAG-ASN         : angle       2.11146 (    6)
  hydrogen bonds       : bond        0.03996 (  616)
  hydrogen bonds       : angle       4.57942 ( 1755)
  SS BOND              : bond        0.00122 (    5)
  SS BOND              : angle       0.76597 (   10)
  covalent geometry    : bond        0.00331 ( 9702)
  covalent geometry    : angle       0.66555 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 189
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.7704 (mmm) cc_final: 0.7080 (mmp)
REVERT: A  389 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7289 (tmm)
REVERT: A  648 MET cc_start: 0.6525 (mmp) cc_final: 0.5884 (tpt)
REVERT: A  733 PHE cc_start: 0.7660 (m-80) cc_final: 0.7379 (m-80)
REVERT: A 1174 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7475 (m-80)
REVERT: A 1218 GLU cc_start: 0.7925 (pp20) cc_final: 0.7675 (pp20)
REVERT: A 1483 MET cc_start: 0.7207 (ttt) cc_final: 0.6803 (ptt)
REVERT: A 1504 MET cc_start: 0.8598 (mtm) cc_final: 0.8184 (mtp)
REVERT: A 1636 LEU cc_start: 0.9183 (tt) cc_final: 0.8916 (tp)
REVERT: A 1655 MET cc_start: 0.7904 (mtm) cc_final: 0.7463 (mtp)
REVERT: A 1686 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.7883 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 194
  average time/residue: 0.1670
  time to fit residues: 49.1277
Evaluate side-chains
  194 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1393 VAL
Chi-restraints excluded: chain A residue 1525 MET
Chi-restraints excluded: chain A residue 1686 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 816 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.210520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.155888 restraints weight = 26722.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 3.12
r_work: 0.3636 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9709  Z= 0.150
  Angle     :  0.659  14.135  13146  Z= 0.331
  Chirality :  0.042   0.272   1535
  Planarity :  0.004   0.047   1577
  Dihedral  :  8.135  58.309   1807
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.39 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1130
  helix:  1.28 (0.19), residues: 781
  sheet:  None (None), residues: 0
  loop : -1.75 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1551 
 HIS   0.003   0.001   HIS A1358 
 PHE   0.020   0.002   PHE A 125 
 TYR   0.025   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A 743 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    2)
  link_NAG-ASN         : angle       2.10209 (    6)
  hydrogen bonds       : bond        0.03959 (  616)
  hydrogen bonds       : angle       4.58275 ( 1755)
  SS BOND              : bond        0.00129 (    5)
  SS BOND              : angle       0.77842 (   10)
  covalent geometry    : bond        0.00346 ( 9702)
  covalent geometry    : angle       0.65741 (13130)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 0.917 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.7705 (mmm) cc_final: 0.7110 (mmp)
REVERT: A  134 MET cc_start: 0.8036 (mpp) cc_final: 0.7584 (mpp)
REVERT: A  389 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7275 (tmm)
REVERT: A  648 MET cc_start: 0.6669 (mmp) cc_final: 0.6023 (tpt)
REVERT: A  733 PHE cc_start: 0.7583 (m-80) cc_final: 0.7313 (m-80)
REVERT: A 1174 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7508 (m-80)
REVERT: A 1179 PHE cc_start: 0.8833 (m-80) cc_final: 0.8502 (m-80)
REVERT: A 1218 GLU cc_start: 0.7890 (pp20) cc_final: 0.7617 (pp20)
REVERT: A 1434 PHE cc_start: 0.8511 (t80) cc_final: 0.8262 (t80)
REVERT: A 1504 MET cc_start: 0.8594 (mtm) cc_final: 0.8181 (mtp)
REVERT: A 1636 LEU cc_start: 0.9188 (tt) cc_final: 0.8924 (tp)
REVERT: A 1655 MET cc_start: 0.7894 (mtm) cc_final: 0.7487 (mtp)
REVERT: A 1686 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.7816 (m-30)
REVERT: A 1730 MET cc_start: 0.8052 (mmm) cc_final: 0.7832 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 189
  average time/residue: 0.1725
  time to fit residues: 49.4792
Evaluate side-chains
  194 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  659 ILE
Chi-restraints excluded: chain A residue 1174 TYR
Chi-restraints excluded: chain A residue 1279 THR
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1350 MET
Chi-restraints excluded: chain A residue 1393 VAL
Chi-restraints excluded: chain A residue 1525 MET
Chi-restraints excluded: chain A residue 1686 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 19 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4433 r_free = 0.4433 target = 0.210267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.151228 restraints weight = 16315.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.79
r_work: 0.3609 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9709  Z= 0.148
  Angle     :  0.657  14.076  13146  Z= 0.331
  Chirality :  0.043   0.260   1535
  Planarity :  0.004   0.047   1577
  Dihedral  :  8.095  58.723   1807
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.79 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1130
  helix:  1.31 (0.19), residues: 781
  sheet:  None (None), residues: 0
  loop : -1.76 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1551 
 HIS   0.003   0.001   HIS A1358 
 PHE   0.029   0.002   PHE A 125 
 TYR   0.035   0.002   TYR A 364 
 ARG   0.004   0.000   ARG A1355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00377 (    2)
  link_NAG-ASN         : angle       2.06484 (    6)
  hydrogen bonds       : bond        0.03971 (  616)
  hydrogen bonds       : angle       4.57298 ( 1755)
  SS BOND              : bond        0.00130 (    5)
  SS BOND              : angle       0.77171 (   10)
  covalent geometry    : bond        0.00339 ( 9702)
  covalent geometry    : angle       0.65571 (13130)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6445.37 seconds
wall clock time: 114 minutes 36.06 seconds (6876.06 seconds total)