Starting phenix.real_space_refine
on Sun May  3 01:48:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vrb_65282/05_2026/9vrb_65282.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      54      5.16       5
     C    6117      2.51       5
     N    1615      2.21       5
     O    1762      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9556
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1212, 9492
          Classifications: {'peptide': 1212}
          Link IDs: {'PTRANS': 47, 'TRANS': 1164}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.12, per 1000 atoms: 0.22
  Number of scatterers: 9556
  At special positions: 0
  Unit cell: (75.33, 87.42, 139.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       6     15.00
     Mg      2     11.99
     O    1762      8.00
     N    1615      7.00
     C    6117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 319.9 milliseconds
  

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      69.4% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 235 through 242
    Processing helix  chain 'A' and resid 245 through 255
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 284
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.545A  pdb=" N   GLU A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 304
    Processing helix  chain 'A' and resid 304 through 323
      removed outlier: 3.805A  pdb=" N   TYR A 323 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 328 through 338
    Processing helix  chain 'A' and resid 346 through 391
      removed outlier: 3.954A  pdb=" N   PHE A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE A 354 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
      removed outlier: 3.924A  pdb=" N   SER A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 419
      removed outlier: 4.417A  pdb=" N   VAL A 414 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLN A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 424
    Processing helix  chain 'A' and resid 425 through 445
      Proline residue:  A 431  - end of helix
    Processing helix  chain 'A' and resid 448 through 462
      removed outlier: 3.634A  pdb=" N   THR A 452 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 494
    Processing helix  chain 'A' and resid 494 through 502
    Processing helix  chain 'A' and resid 503 through 554
      removed outlier: 3.735A  pdb=" N   TRP A 521 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      Proline residue:  A 540  - end of helix
    Processing helix  chain 'A' and resid 559 through 602
      removed outlier: 4.388A  pdb=" N   GLU A 575 " --> pdb=" O   ARG A 571 " (cutoff:3.500A)
      Proline residue:  A 576  - end of helix
      Proline residue:  A 581  - end of helix
    Processing helix  chain 'A' and resid 663 through 673
    Processing helix  chain 'A' and resid 702 through 708
    Processing helix  chain 'A' and resid 713 through 724
    Processing helix  chain 'A' and resid 726 through 733
    Processing helix  chain 'A' and resid 735 through 738
    Processing helix  chain 'A' and resid 742 through 746
    Processing helix  chain 'A' and resid 749 through 764
      removed outlier: 3.573A  pdb=" N   GLN A 764 " --> pdb=" O   ARG A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 791
    Processing helix  chain 'A' and resid 806 through 810
    Processing helix  chain 'A' and resid 830 through 834
      removed outlier: 3.533A  pdb=" N   LEU A 833 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A 834 " --> pdb=" O   ASP A 831 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 830 through 834'
    Processing helix  chain 'A' and resid 838 through 852
    Processing helix  chain 'A' and resid 925 through 935
      removed outlier: 3.950A  pdb=" N   VAL A 929 " --> pdb=" O   VAL A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 937 through 940
    Processing helix  chain 'A' and resid 941 through 967
      removed outlier: 3.714A  pdb=" N   LEU A 945 " --> pdb=" O   THR A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 1025
    Processing helix  chain 'A' and resid 1028 through 1035
      removed outlier: 3.755A  pdb=" N   PHE A1032 " --> pdb=" O   PRO A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1054
      removed outlier: 3.865A  pdb=" N   ILE A1040 " --> pdb=" O   PRO A1036 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP A1047 " --> pdb=" O   ARG A1043 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLN A1048 " --> pdb=" O   VAL A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1080
    Processing helix  chain 'A' and resid 1083 through 1129
      Proline residue:  A1089  - end of helix
      removed outlier: 4.142A  pdb=" N   SER A1104 " --> pdb=" O   TYR A1100 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLU A1107 " --> pdb=" O   ALA A1103 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER A1117 " --> pdb=" O   SER A1113 " (cutoff:3.500A)
      Proline residue:  A1118  - end of helix
    Processing helix  chain 'A' and resid 1129 through 1136
    Processing helix  chain 'A' and resid 1138 through 1189
      Proline residue:  A1156  - end of helix
      removed outlier: 3.536A  pdb=" N   GLU A1165 " --> pdb=" O   LEU A1161 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A1177 " --> pdb=" O   LEU A1173 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE A1189 " --> pdb=" O   ILE A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1207
    Processing helix  chain 'A' and resid 1208 through 1237
      removed outlier: 3.746A  pdb=" N   ARG A1226 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A1228 " --> pdb=" O   GLU A1224 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   SER A1229 " --> pdb=" O   ASN A1225 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A1230 " --> pdb=" O   ARG A1226 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR A1236 " --> pdb=" O   ARG A1232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1309
      removed outlier: 3.910A  pdb=" N   LEU A1309 " --> pdb=" O   LEU A1305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1337
    Processing helix  chain 'A' and resid 1353 through 1358
    Processing helix  chain 'A' and resid 1364 through 1375
    Processing helix  chain 'A' and resid 1377 through 1383
    Processing helix  chain 'A' and resid 1393 through 1397
    Processing helix  chain 'A' and resid 1400 through 1415
    Processing helix  chain 'A' and resid 1430 through 1445
      removed outlier: 3.966A  pdb=" N   LEU A1436 " --> pdb=" O   ALA A1432 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LYS A1439 " --> pdb=" O   ASN A1435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1456 through 1461
      removed outlier: 3.784A  pdb=" N   VAL A1460 " --> pdb=" O   ARG A1456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1479 through 1486
    Processing helix  chain 'A' and resid 1489 through 1500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 613
      removed outlier: 5.843A  pdb=" N   ILE A 612 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LYS A 677 " --> pdb=" O   PHE A 630 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE A 630 " --> pdb=" O   LYS A 677 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   CYS A 679 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ALA A 628 " --> pdb=" O   CYS A 679 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 623 " --> pdb=" O   VAL A 648 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   ILE A 644 " --> pdb=" O   ASP A 627 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   THR A 629 " --> pdb=" O   SER A 642 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   SER A 642 " --> pdb=" O   THR A 629 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 688 through 691
      removed outlier: 6.222A  pdb=" N   TYR A 769 " --> pdb=" O   ILE A 801 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   VAL A 803 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU A 771 " --> pdb=" O   VAL A 803 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A 826 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LYS A 820 " --> pdb=" O   ILE A 824 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ILE A 824 " --> pdb=" O   LYS A 820 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 701
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1279 through 1286
      removed outlier: 6.088A  pdb=" N   HIS A1280 " --> pdb=" O   VAL A1269 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   VAL A1269 " --> pdb=" O   HIS A1280 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   CYS A1284 " --> pdb=" O   VAL A1265 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   VAL A1265 " --> pdb=" O   CYS A1284 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   PHE A1286 " --> pdb=" O   GLU A1263 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   GLU A1263 " --> pdb=" O   PHE A1286 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU A1267 " --> pdb=" O   GLY A1317 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLY A1317 " --> pdb=" O   LEU A1267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1339 through 1342
      removed outlier: 7.074A  pdb=" N   LEU A1420 " --> pdb=" O   CYS A1451 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   ILE A1453 " --> pdb=" O   LEU A1420 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LEU A1422 " --> pdb=" O   ILE A1453 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER A1470 " --> pdb=" O   ILE A1474 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   ILE A1474 " --> pdb=" O   SER A1470 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1351 through 1352

    628 hydrogen bonds defined for protein.
    1833 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.69

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1540
        1.32 -     1.44: 2529
        1.44 -     1.57: 5581
        1.57 -     1.69: 10
        1.69 -     1.81: 88
  Bond restraints: 9748
  Sorted by residual:
  bond pdb=" C   LYS A1116 "
       pdb=" O   LYS A1116 "
    ideal  model  delta    sigma   weight residual
    1.236  1.195  0.041 1.32e-02 5.74e+03 9.84e+00
  bond pdb=" CA  LYS A1116 "
       pdb=" C   LYS A1116 "
    ideal  model  delta    sigma   weight residual
    1.522  1.484  0.037 1.37e-02 5.33e+03 7.47e+00
  bond pdb=" C   GLN A1115 "
       pdb=" N   LYS A1116 "
    ideal  model  delta    sigma   weight residual
    1.333  1.293  0.040 1.55e-02 4.16e+03 6.50e+00
  bond pdb=" CA  LYS A1116 "
       pdb=" CB  LYS A1116 "
    ideal  model  delta    sigma   weight residual
    1.532  1.505  0.027 1.65e-02 3.67e+03 2.69e+00
  bond pdb=" C   THR A 638 "
       pdb=" N   PRO A 639 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.25e-02 6.40e+03 1.48e+00
  ... (remaining 9743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 12836
        1.38 -     2.75: 305
        2.75 -     4.13: 70
        4.13 -     5.50: 22
        5.50 -     6.88: 4
  Bond angle restraints: 13237
  Sorted by residual:
  angle pdb=" N   ILE A1055 "
        pdb=" CA  ILE A1055 "
        pdb=" C   ILE A1055 "
      ideal   model   delta    sigma   weight residual
     111.56  108.17    3.39 8.60e-01 1.35e+00 1.56e+01
  angle pdb=" N   LYS A1387 "
        pdb=" CA  LYS A1387 "
        pdb=" CB  LYS A1387 "
      ideal   model   delta    sigma   weight residual
     114.17  110.28    3.89 1.14e+00 7.69e-01 1.16e+01
  angle pdb=" O   GLN A1115 "
        pdb=" C   GLN A1115 "
        pdb=" N   LYS A1116 "
      ideal   model   delta    sigma   weight residual
     122.43  117.52    4.91 1.46e+00 4.69e-01 1.13e+01
  angle pdb=" CA  GLN A1115 "
        pdb=" C   GLN A1115 "
        pdb=" N   LYS A1116 "
      ideal   model   delta    sigma   weight residual
     118.41  122.88   -4.47 1.34e+00 5.57e-01 1.11e+01
  angle pdb=" C3' ATP A1601 "
        pdb=" C4' ATP A1601 "
        pdb=" C5' ATP A1601 "
      ideal   model   delta    sigma   weight residual
     115.19  110.15    5.04 1.76e+00 3.23e-01 8.21e+00
  ... (remaining 13232 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 5270
       17.78 -    35.55: 476
       35.55 -    53.33: 135
       53.33 -    71.10: 18
       71.10 -    88.88: 7
  Dihedral angle restraints: 5906
    sinusoidal: 2381
      harmonic: 3525
  Sorted by residual:
  dihedral pdb=" CA  LYS A1387 "
           pdb=" C   LYS A1387 "
           pdb=" N   LEU A1388 "
           pdb=" CA  LEU A1388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.17   20.83     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ASP A1052 "
           pdb=" C   ASP A1052 "
           pdb=" N   LEU A1053 "
           pdb=" CA  LEU A1053 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.08  -15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CG  ARG A 788 "
           pdb=" CD  ARG A 788 "
           pdb=" NE  ARG A 788 "
           pdb=" CZ  ARG A 788 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.04   42.96     2      1.50e+01 4.44e-03 9.91e+00
  ... (remaining 5903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1352
       0.059 -    0.119: 163
       0.119 -    0.178: 17
       0.178 -    0.238: 2
       0.238 -    0.297: 4
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" C2' ATP A1601 "
            pdb=" C1' ATP A1601 "
            pdb=" C3' ATP A1601 "
            pdb=" O2' ATP A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" C2' ATP A1602 "
            pdb=" C1' ATP A1602 "
            pdb=" C3' ATP A1602 "
            pdb=" O2' ATP A1602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C3' ATP A1602 "
            pdb=" C2' ATP A1602 "
            pdb=" C4' ATP A1602 "
            pdb=" O3' ATP A1602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.88    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1535 not shown)

  Planarity restraints: 1652
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 968 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO A 969 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 969 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 969 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1115 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   GLN A1115 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLN A1115 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A1116 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 716 "   -0.154 9.50e-02 1.11e+02   6.93e-02 3.34e+00
        pdb=" NE  ARG A 716 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 716 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 716 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 716 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1649 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 13
        2.51 -     3.10: 7021
        3.10 -     3.70: 15112
        3.70 -     4.30: 22966
        4.30 -     4.90: 37541
  Nonbonded interactions: 82653
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 665 "
            pdb="MG    MG A1603 "
     model   vdw
     1.907 2.170
  nonbonded pdb=" OE1 GLN A1344 "
            pdb="MG    MG A1604 "
     model   vdw
     1.982 2.170
  nonbonded pdb=" OG  SER A1303 "
            pdb="MG    MG A1604 "
     model   vdw
     1.996 2.170
  nonbonded pdb=" O2B ATP A1601 "
            pdb="MG    MG A1603 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" OE1 GLN A 693 "
            pdb="MG    MG A1603 "
     model   vdw
     2.082 2.170
  ... (remaining 82648 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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      :  0.003   0.041   9748  Z= 0.156
  Angle     :  0.588   6.879  13237  Z= 0.328
  Chirality :  0.042   0.297   1538
  Planarity :  0.005   0.069   1652
  Dihedral  : 14.983  88.878   3628
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  8.55 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.24), residues: 1208
  helix:  1.45 (0.18), residues: 790
  sheet: -1.61 (0.50), residues: 74
  loop :  0.31 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 716 
 TYR   0.009   0.001   TYR A 231 
 PHE   0.011   0.001   PHE A 354 
 TRP   0.022   0.001   TRP A1081 
 HIS   0.002   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9748)
  covalent geometry    : angle       0.58823 (13237)
  hydrogen bonds       : bond        0.11918 (  628)
  hydrogen bonds       : angle       5.37072 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8626 (mmm) cc_final: 0.8191 (mmm)
REVERT: A  415 GLN cc_start: 0.7840 (tp40) cc_final: 0.7058 (tp-100)
REVERT: A  616 HIS cc_start: 0.8370 (t-90) cc_final: 0.8154 (t-170)
REVERT: A  952 MET cc_start: 0.7972 (mmm) cc_final: 0.7657 (mmm)
REVERT: A  957 GLN cc_start: 0.7794 (mm110) cc_final: 0.7516 (mm110)
REVERT: A 1003 LEU cc_start: 0.7936 (mm) cc_final: 0.7675 (tp)
REVERT: A 1140 LYS cc_start: 0.8402 (mttt) cc_final: 0.7704 (mmpt)
REVERT: A 1226 ARG cc_start: 0.7020 (mtp85) cc_final: 0.6523 (mtt90)
REVERT: A 1266 ASP cc_start: 0.8087 (m-30) cc_final: 0.7824 (m-30)
REVERT: A 1273 ASP cc_start: 0.8097 (m-30) cc_final: 0.7714 (m-30)
REVERT: A 1355 MET cc_start: 0.8054 (mtp) cc_final: 0.6976 (tmt)
REVERT: A 1395 ASN cc_start: 0.8470 (m-40) cc_final: 0.8092 (m110)
REVERT: A 1498 TYR cc_start: 0.7808 (t80) cc_final: 0.7497 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 127
  average time/residue: 0.7196
  time to fit residues: 96.4490
Evaluate side-chains
  125 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue 1055 ILE
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A1210 ASN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.128988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.102766 restraints weight = 9425.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.31
r_work: 0.2942 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.0606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9748  Z= 0.168
  Angle     :  0.516   6.286  13237  Z= 0.272
  Chirality :  0.041   0.140   1538
  Planarity :  0.005   0.058   1652
  Dihedral  :  8.541  84.562   1393
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.93 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.24), residues: 1208
  helix:  1.76 (0.18), residues: 786
  sheet: -0.78 (0.60), residues: 64
  loop :  0.24 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 716 
 TYR   0.011   0.002   TYR A1100 
 PHE   0.010   0.001   PHE A1017 
 TRP   0.017   0.002   TRP A1081 
 HIS   0.003   0.001   HIS A1121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9748)
  covalent geometry    : angle       0.51625 (13237)
  hydrogen bonds       : bond        0.05053 (  628)
  hydrogen bonds       : angle       4.31775 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8708 (mmm) cc_final: 0.8382 (mmm)
REVERT: A  293 GLU cc_start: 0.7513 (pt0) cc_final: 0.6828 (mm-30)
REVERT: A  415 GLN cc_start: 0.7975 (tp40) cc_final: 0.7222 (tp-100)
REVERT: A  744 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7874 (mtt90)
REVERT: A  957 GLN cc_start: 0.7849 (mm110) cc_final: 0.7630 (mm110)
REVERT: A 1003 LEU cc_start: 0.7991 (mm) cc_final: 0.7730 (tp)
REVERT: A 1140 LYS cc_start: 0.8482 (mttt) cc_final: 0.7741 (mmpt)
REVERT: A 1226 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6524 (mtt90)
REVERT: A 1266 ASP cc_start: 0.8131 (m-30) cc_final: 0.7854 (m-30)
REVERT: A 1273 ASP cc_start: 0.8061 (m-30) cc_final: 0.7736 (m-30)
REVERT: A 1355 MET cc_start: 0.8162 (mtp) cc_final: 0.7095 (tmt)
REVERT: A 1498 TYR cc_start: 0.7809 (t80) cc_final: 0.7511 (t80)
  outliers start: 18
  outliers final: 6
  residues processed: 131
  average time/residue: 0.7183
  time to fit residues: 99.1348
Evaluate side-chains
  122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  493 LYS
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue 1049 SER
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1298 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0170
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1333 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.130490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.104174 restraints weight = 9423.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.31
r_work: 0.2962 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9748  Z= 0.129
  Angle     :  0.475   5.869  13237  Z= 0.250
  Chirality :  0.040   0.130   1538
  Planarity :  0.004   0.054   1652
  Dihedral  :  8.021  76.683   1384
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.61 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.24), residues: 1208
  helix:  2.01 (0.18), residues: 788
  sheet: -0.60 (0.61), residues: 64
  loop :  0.24 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 231 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.016   0.001   TRP A1081 
 HIS   0.002   0.001   HIS A1121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9748)
  covalent geometry    : angle       0.47501 (13237)
  hydrogen bonds       : bond        0.04536 (  628)
  hydrogen bonds       : angle       4.07810 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8684 (mmm) cc_final: 0.8392 (mmm)
REVERT: A  293 GLU cc_start: 0.7521 (pt0) cc_final: 0.6824 (mm-30)
REVERT: A  415 GLN cc_start: 0.7947 (tp40) cc_final: 0.7169 (tp-100)
REVERT: A  585 SER cc_start: 0.8548 (t) cc_final: 0.8231 (p)
REVERT: A  681 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7642 (mp10)
REVERT: A 1003 LEU cc_start: 0.7984 (mm) cc_final: 0.7727 (tp)
REVERT: A 1140 LYS cc_start: 0.8454 (mttt) cc_final: 0.7710 (mmpt)
REVERT: A 1266 ASP cc_start: 0.8077 (m-30) cc_final: 0.7811 (m-30)
REVERT: A 1273 ASP cc_start: 0.8023 (m-30) cc_final: 0.7697 (m-30)
REVERT: A 1355 MET cc_start: 0.8117 (mtp) cc_final: 0.7023 (tmt)
REVERT: A 1498 TYR cc_start: 0.7783 (t80) cc_final: 0.7470 (t80)
  outliers start: 20
  outliers final: 6
  residues processed: 141
  average time/residue: 0.7336
  time to fit residues: 109.1579
Evaluate side-chains
  125 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   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 311 ASN
A 616 HIS
A 957 GLN
A1333 HIS
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.130489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.104039 restraints weight = 9483.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.33
r_work: 0.2959 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9748  Z= 0.128
  Angle     :  0.472   6.414  13237  Z= 0.246
  Chirality :  0.040   0.195   1538
  Planarity :  0.004   0.051   1652
  Dihedral  :  7.842  76.056   1382
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.95 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.24), residues: 1208
  helix:  2.13 (0.18), residues: 787
  sheet: -0.55 (0.61), residues: 64
  loop :  0.28 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.009   0.001   TYR A 802 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.016   0.001   TRP A1081 
 HIS   0.002   0.001   HIS A1121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9748)
  covalent geometry    : angle       0.47230 (13237)
  hydrogen bonds       : bond        0.04433 (  628)
  hydrogen bonds       : angle       4.00686 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8641 (mmm) cc_final: 0.8359 (mmm)
REVERT: A  293 GLU cc_start: 0.7494 (pt0) cc_final: 0.6764 (mm-30)
REVERT: A  415 GLN cc_start: 0.7907 (tp40) cc_final: 0.7138 (tp-100)
REVERT: A  585 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8283 (p)
REVERT: A  638 THR cc_start: 0.8465 (p) cc_final: 0.8126 (t)
REVERT: A  681 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7630 (mp10)
REVERT: A 1003 LEU cc_start: 0.7970 (mm) cc_final: 0.7717 (tp)
REVERT: A 1140 LYS cc_start: 0.8447 (mttt) cc_final: 0.7699 (mmpt)
REVERT: A 1266 ASP cc_start: 0.8105 (m-30) cc_final: 0.7835 (m-30)
REVERT: A 1273 ASP cc_start: 0.8003 (m-30) cc_final: 0.7702 (m-30)
REVERT: A 1282 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8344 (mm)
REVERT: A 1355 MET cc_start: 0.8144 (mtp) cc_final: 0.7017 (tmt)
REVERT: A 1498 TYR cc_start: 0.7804 (t80) cc_final: 0.7500 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 131
  average time/residue: 0.7093
  time to fit residues: 98.2251
Evaluate side-chains
  126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1282 ILE
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1333 HIS
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.130653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.104212 restraints weight = 9458.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.34
r_work: 0.2970 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9748  Z= 0.132
  Angle     :  0.477   7.629  13237  Z= 0.247
  Chirality :  0.040   0.203   1538
  Planarity :  0.004   0.049   1652
  Dihedral  :  7.871  75.258   1382
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.53 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.24), residues: 1208
  helix:  2.20 (0.18), residues: 787
  sheet: -0.47 (0.60), residues: 64
  loop :  0.30 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 802 
 PHE   0.009   0.001   PHE A1142 
 TRP   0.017   0.001   TRP A1081 
 HIS   0.003   0.001   HIS A1333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9748)
  covalent geometry    : angle       0.47650 (13237)
  hydrogen bonds       : bond        0.04437 (  628)
  hydrogen bonds       : angle       3.96784 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8708 (mmm) cc_final: 0.8417 (mmm)
REVERT: A  293 GLU cc_start: 0.7496 (pt0) cc_final: 0.6789 (mm-30)
REVERT: A  415 GLN cc_start: 0.8054 (tp40) cc_final: 0.7327 (tp-100)
REVERT: A  505 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8482 (m-30)
REVERT: A  585 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8348 (p)
REVERT: A  638 THR cc_start: 0.8486 (p) cc_final: 0.8156 (t)
REVERT: A  652 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8468 (mtt)
REVERT: A  681 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7688 (mp10)
REVERT: A 1003 LEU cc_start: 0.8064 (mm) cc_final: 0.7823 (tp)
REVERT: A 1140 LYS cc_start: 0.8473 (mttt) cc_final: 0.7766 (mmpt)
REVERT: A 1266 ASP cc_start: 0.8151 (m-30) cc_final: 0.7889 (m-30)
REVERT: A 1273 ASP cc_start: 0.8019 (m-30) cc_final: 0.7758 (m-30)
REVERT: A 1282 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8406 (mm)
REVERT: A 1355 MET cc_start: 0.8195 (mtp) cc_final: 0.7149 (tmt)
REVERT: A 1481 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7239 (tp40)
REVERT: A 1498 TYR cc_start: 0.7896 (t80) cc_final: 0.7589 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 131
  average time/residue: 0.6673
  time to fit residues: 92.5260
Evaluate side-chains
  133 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1282 ILE
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0020
   chunk 88 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1333 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.130031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104031 restraints weight = 9463.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.30
r_work: 0.2948 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9748  Z= 0.131
  Angle     :  0.482   9.384  13237  Z= 0.248
  Chirality :  0.040   0.223   1538
  Planarity :  0.004   0.047   1652
  Dihedral  :  7.854  74.934   1382
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.91 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.24), residues: 1208
  helix:  2.29 (0.18), residues: 781
  sheet: -0.44 (0.60), residues: 64
  loop :  0.37 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 802 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.020   0.001   TRP A1081 
 HIS   0.003   0.001   HIS A1333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9748)
  covalent geometry    : angle       0.48211 (13237)
  hydrogen bonds       : bond        0.04422 (  628)
  hydrogen bonds       : angle       3.95762 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8693 (mmm) cc_final: 0.8323 (mmm)
REVERT: A  293 GLU cc_start: 0.7473 (pt0) cc_final: 0.6749 (mm-30)
REVERT: A  415 GLN cc_start: 0.8018 (tp40) cc_final: 0.7264 (tp-100)
REVERT: A  585 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (p)
REVERT: A  638 THR cc_start: 0.8474 (p) cc_final: 0.8141 (t)
REVERT: A  652 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (mtt)
REVERT: A  681 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7616 (mp10)
REVERT: A 1003 LEU cc_start: 0.8009 (mm) cc_final: 0.7758 (tp)
REVERT: A 1140 LYS cc_start: 0.8445 (mttt) cc_final: 0.7700 (mmpt)
REVERT: A 1266 ASP cc_start: 0.8130 (m-30) cc_final: 0.7867 (m-30)
REVERT: A 1273 ASP cc_start: 0.8002 (m-30) cc_final: 0.7764 (m-30)
REVERT: A 1282 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8372 (mm)
REVERT: A 1355 MET cc_start: 0.8140 (mtp) cc_final: 0.7044 (tmt)
REVERT: A 1366 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7081 (tm-30)
REVERT: A 1481 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7172 (tp40)
REVERT: A 1498 TYR cc_start: 0.7820 (t80) cc_final: 0.7515 (t80)
  outliers start: 20
  outliers final: 8
  residues processed: 133
  average time/residue: 0.6533
  time to fit residues: 92.2484
Evaluate side-chains
  135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1282 ILE
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 120 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 118 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.130057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.103541 restraints weight = 9480.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.33
r_work: 0.2966 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9748  Z= 0.128
  Angle     :  0.483   9.915  13237  Z= 0.248
  Chirality :  0.040   0.228   1538
  Planarity :  0.004   0.046   1652
  Dihedral  :  7.830  74.224   1382
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.30 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.24), residues: 1208
  helix:  2.31 (0.18), residues: 782
  sheet: -0.39 (0.59), residues: 64
  loop :  0.37 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 802 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.022   0.001   TRP A1081 
 HIS   0.002   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9748)
  covalent geometry    : angle       0.48316 (13237)
  hydrogen bonds       : bond        0.04376 (  628)
  hydrogen bonds       : angle       3.94522 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8703 (mmm) cc_final: 0.8330 (mmm)
REVERT: A  293 GLU cc_start: 0.7454 (pt0) cc_final: 0.6759 (mm-30)
REVERT: A  415 GLN cc_start: 0.8054 (tp40) cc_final: 0.7304 (tp-100)
REVERT: A  585 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8315 (p)
REVERT: A  638 THR cc_start: 0.8486 (p) cc_final: 0.8158 (t)
REVERT: A  652 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8452 (mtt)
REVERT: A  681 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7622 (mp10)
REVERT: A 1003 LEU cc_start: 0.8027 (mm) cc_final: 0.7781 (tp)
REVERT: A 1140 LYS cc_start: 0.8441 (mttt) cc_final: 0.7729 (mmpt)
REVERT: A 1266 ASP cc_start: 0.8118 (m-30) cc_final: 0.7855 (m-30)
REVERT: A 1273 ASP cc_start: 0.7976 (m-30) cc_final: 0.7761 (m-30)
REVERT: A 1282 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8393 (mm)
REVERT: A 1355 MET cc_start: 0.8161 (mtp) cc_final: 0.7085 (tmt)
REVERT: A 1366 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7115 (tm-30)
REVERT: A 1395 ASN cc_start: 0.8692 (m-40) cc_final: 0.8202 (m110)
REVERT: A 1481 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7218 (tp40)
REVERT: A 1498 TYR cc_start: 0.7871 (t80) cc_final: 0.7564 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 131
  average time/residue: 0.6568
  time to fit residues: 91.0138
Evaluate side-chains
  136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1282 ILE
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 119 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1333 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.130610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.104180 restraints weight = 9386.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.33
r_work: 0.2973 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9748  Z= 0.128
  Angle     :  0.483   9.152  13237  Z= 0.249
  Chirality :  0.040   0.214   1538
  Planarity :  0.004   0.045   1652
  Dihedral  :  7.820  74.185   1382
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.78 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.24), residues: 1208
  helix:  2.34 (0.18), residues: 781
  sheet: -0.38 (0.59), residues: 64
  loop :  0.39 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 802 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.025   0.001   TRP A1081 
 HIS   0.004   0.001   HIS A1333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9748)
  covalent geometry    : angle       0.48335 (13237)
  hydrogen bonds       : bond        0.04355 (  628)
  hydrogen bonds       : angle       3.93816 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8708 (mmm) cc_final: 0.8336 (mmm)
REVERT: A  293 GLU cc_start: 0.7443 (pt0) cc_final: 0.6756 (mm-30)
REVERT: A  415 GLN cc_start: 0.8070 (tp40) cc_final: 0.7320 (tp-100)
REVERT: A  585 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8330 (p)
REVERT: A  638 THR cc_start: 0.8474 (p) cc_final: 0.8156 (t)
REVERT: A  652 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8446 (mtt)
REVERT: A  681 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7622 (mp10)
REVERT: A 1003 LEU cc_start: 0.8020 (mm) cc_final: 0.7776 (tp)
REVERT: A 1140 LYS cc_start: 0.8436 (mttt) cc_final: 0.7732 (mmpt)
REVERT: A 1171 MET cc_start: 0.7573 (mmm) cc_final: 0.7085 (mmm)
REVERT: A 1218 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7888 (tt)
REVERT: A 1266 ASP cc_start: 0.8138 (m-30) cc_final: 0.7885 (m-30)
REVERT: A 1273 ASP cc_start: 0.7971 (m-30) cc_final: 0.7752 (m-30)
REVERT: A 1355 MET cc_start: 0.8140 (mtp) cc_final: 0.7083 (tmt)
REVERT: A 1366 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7157 (tm-30)
REVERT: A 1379 GLU cc_start: 0.6992 (tp30) cc_final: 0.6776 (tp30)
REVERT: A 1395 ASN cc_start: 0.8692 (m-40) cc_final: 0.8189 (m110)
REVERT: A 1481 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7295 (tp40)
  outliers start: 19
  outliers final: 9
  residues processed: 133
  average time/residue: 0.6517
  time to fit residues: 91.8675
Evaluate side-chains
  135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  652 MET
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0570
   chunk 96 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 115 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1048 GLN
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.131609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.105171 restraints weight = 9447.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.33
r_work: 0.2992 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9748  Z= 0.109
  Angle     :  0.463   8.727  13237  Z= 0.239
  Chirality :  0.040   0.201   1538
  Planarity :  0.004   0.045   1652
  Dihedral  :  7.630  69.522   1382
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 13.45 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.53 (0.24), residues: 1208
  helix:  2.47 (0.18), residues: 779
  sheet: -0.37 (0.59), residues: 64
  loop :  0.39 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.008   0.001   TYR A 231 
 PHE   0.007   0.001   PHE A 840 
 TRP   0.032   0.001   TRP A1081 
 HIS   0.002   0.001   HIS A 823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9748)
  covalent geometry    : angle       0.46284 (13237)
  hydrogen bonds       : bond        0.04047 (  628)
  hydrogen bonds       : angle       3.85945 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  293 GLU cc_start: 0.7427 (pt0) cc_final: 0.6718 (mm-30)
REVERT: A  415 GLN cc_start: 0.8074 (tp40) cc_final: 0.7320 (tp-100)
REVERT: A  585 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8302 (p)
REVERT: A  638 THR cc_start: 0.8384 (p) cc_final: 0.8108 (t)
REVERT: A  681 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7590 (mp10)
REVERT: A  964 MET cc_start: 0.8731 (mmm) cc_final: 0.8227 (tpt)
REVERT: A 1003 LEU cc_start: 0.7987 (mm) cc_final: 0.7738 (tp)
REVERT: A 1110 ARG cc_start: 0.7337 (mtt90) cc_final: 0.6878 (mtm-85)
REVERT: A 1140 LYS cc_start: 0.8427 (mttt) cc_final: 0.7692 (mmpt)
REVERT: A 1210 ASN cc_start: 0.7501 (p0) cc_final: 0.6727 (OUTLIER)
REVERT: A 1218 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7822 (tt)
REVERT: A 1266 ASP cc_start: 0.8139 (m-30) cc_final: 0.7882 (m-30)
REVERT: A 1282 ILE cc_start: 0.8702 (mt) cc_final: 0.8365 (mm)
REVERT: A 1355 MET cc_start: 0.8076 (mtp) cc_final: 0.7004 (tmt)
REVERT: A 1379 GLU cc_start: 0.6947 (tp30) cc_final: 0.6727 (tp30)
REVERT: A 1395 ASN cc_start: 0.8606 (m-40) cc_final: 0.8212 (m110)
REVERT: A 1481 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7197 (tp40)
  outliers start: 13
  outliers final: 8
  residues processed: 131
  average time/residue: 0.6967
  time to fit residues: 96.7839
Evaluate side-chains
  132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.104443 restraints weight = 9352.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.33
r_work: 0.2974 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9748  Z= 0.136
  Angle     :  0.495   9.653  13237  Z= 0.254
  Chirality :  0.041   0.235   1538
  Planarity :  0.004   0.045   1652
  Dihedral  :  7.830  75.490   1382
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.02 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.24), residues: 1208
  helix:  2.35 (0.18), residues: 780
  sheet: -0.35 (0.59), residues: 64
  loop :  0.39 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.010   0.001   TYR A 802 
 PHE   0.009   0.001   PHE A1142 
 TRP   0.033   0.002   TRP A1081 
 HIS   0.002   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9748)
  covalent geometry    : angle       0.49512 (13237)
  hydrogen bonds       : bond        0.04377 (  628)
  hydrogen bonds       : angle       3.93823 ( 1833)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8711 (mmm) cc_final: 0.8317 (mmm)
REVERT: A  293 GLU cc_start: 0.7435 (pt0) cc_final: 0.6771 (mm-30)
REVERT: A  415 GLN cc_start: 0.8100 (tp40) cc_final: 0.7353 (tp-100)
REVERT: A  585 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8342 (p)
REVERT: A  638 THR cc_start: 0.8415 (p) cc_final: 0.8133 (t)
REVERT: A  681 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7609 (mp10)
REVERT: A 1140 LYS cc_start: 0.8439 (mttt) cc_final: 0.7732 (mmpt)
REVERT: A 1218 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7910 (tt)
REVERT: A 1266 ASP cc_start: 0.8143 (m-30) cc_final: 0.7894 (m-30)
REVERT: A 1355 MET cc_start: 0.8149 (mtp) cc_final: 0.7092 (tmt)
REVERT: A 1366 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7174 (tm-30)
REVERT: A 1379 GLU cc_start: 0.7029 (tp30) cc_final: 0.6805 (tp30)
REVERT: A 1395 ASN cc_start: 0.8614 (m-40) cc_final: 0.8241 (m110)
REVERT: A 1481 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7256 (tp40)
  outliers start: 13
  outliers final: 6
  residues processed: 128
  average time/residue: 0.6673
  time to fit residues: 90.5296
Evaluate side-chains
  128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain A residue  506 ARG
Chi-restraints excluded: chain A residue  585 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1225 ASN
Chi-restraints excluded: chain A residue 1298 THR
Chi-restraints excluded: chain A residue 1366 GLN
Chi-restraints excluded: chain A residue 1443 SER
Chi-restraints excluded: chain A residue 1481 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0970
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 616 HIS
A1424 GLN
A1435 ASN
A1493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.105582 restraints weight = 9345.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 1.32
r_work: 0.2974 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9748  Z= 0.122
  Angle     :  0.479   8.847  13237  Z= 0.247
  Chirality :  0.040   0.239   1538
  Planarity :  0.004   0.045   1652
  Dihedral  :  7.757  73.478   1382
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.22 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.24), residues: 1208
  helix:  2.41 (0.18), residues: 778
  sheet: -0.34 (0.59), residues: 64
  loop :  0.41 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 716 
 TYR   0.009   0.001   TYR A 231 
 PHE   0.008   0.001   PHE A1142 
 TRP   0.034   0.002   TRP A1081 
 HIS   0.002   0.001   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9748)
  covalent geometry    : angle       0.47870 (13237)
  hydrogen bonds       : bond        0.04230 (  628)
  hydrogen bonds       : angle       3.90963 ( 1833)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3266.11 seconds
wall clock time: 56 minutes 22.90 seconds (3382.90 seconds total)