Starting phenix.real_space_refine
on Thu Jul 31 03:11:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yuy_34115/07_2025/7yuy_34115_neut.cif"
  }
  resolution = 3.5
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      72      5.16       5
     C    8140      2.51       5
     N    2035      2.21       5
     O    2143      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12391
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "F"
      Number of atoms: 12063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1503, 12063
          Classifications: {'peptide': 1503}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 66, 'TRANS': 1436}
          Chain breaks: 10
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 107
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 45
          Unusual residues: {'BGC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 255
          Unusual residues: {'C14': 1, 'D10': 6, 'D12': 3, 'DD9': 7, 'HP6': 7, 'XKP': 1}
          Classifications: {'undetermined': 25}
          Link IDs: {None: 24}
  Time building chain proxies: 7.70, per 1000 atoms: 0.62
  Number of scatterers: 12391
  At special positions: 0
  Unit cell: (101.2, 115, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P       1     15.00
     O    2143      8.00
     N    2035      7.00
     C    8140      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 658 " - pdb=" SG  CYS F 669 " distance=1.77
    Simple disulfide: pdb=" SG  CYS F1328 " - pdb=" SG  CYS F1345 " 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
    BETA1-3
      " BGC C   1 " - " BGC C   2 "
      " BGC C   2 " - " BGC C   3 "
      " BGC C   3 " - " BGC C   4 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F1849 "
  Time building additional restraints: 4.81
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2858

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 4 sheets defined
      60.7% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'F' and resid 160 through 176
      removed outlier: 4.118A  pdb=" N   ILE F 167 " --> pdb=" O   GLN F 163 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 196
      removed outlier: 3.952A  pdb=" N   ASP F 187 " --> pdb=" O   ARG F 183 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ARG F 196 " --> pdb=" O   LEU F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 201 through 214
      removed outlier: 3.733A  pdb=" N   LEU F 207 " --> pdb=" O   ASP F 203 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE F 214 " --> pdb=" O   HIS F 210 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 229
      removed outlier: 3.666A  pdb=" N   LYS F 223 " --> pdb=" O   ALA F 219 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA F 227 " --> pdb=" O   LYS F 223 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 243
      removed outlier: 3.530A  pdb=" N   GLY F 237 " --> pdb=" O   ASP F 233 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 282 through 293
      removed outlier: 4.207A  pdb=" N   ARG F 288 " --> pdb=" O   ALA F 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 294 through 296
      No H-bonds generated for 'chain 'F' and resid 294 through 296'
    Processing helix  chain 'F' and resid 297 through 313
      removed outlier: 3.645A  pdb=" N   VAL F 302 " --> pdb=" O   PRO F 298 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ARG F 303 " --> pdb=" O   LEU F 299 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   HIS F 304 " --> pdb=" O   GLU F 300 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU F 307 " --> pdb=" O   ARG F 303 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR F 308 " --> pdb=" O   HIS F 304 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 321 through 337
      removed outlier: 3.897A  pdb=" N   LEU F 325 " --> pdb=" O   THR F 321 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 339 through 344
      removed outlier: 4.297A  pdb=" N   GLN F 343 " --> pdb=" O   PRO F 339 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ARG F 344 " --> pdb=" O   LEU F 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 339 through 344'
    Processing helix  chain 'F' and resid 351 through 357
      removed outlier: 3.570A  pdb=" N   ASN F 355 " --> pdb=" O   GLY F 351 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL F 357 " --> pdb=" O   PHE F 353 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 358 through 368
    Processing helix  chain 'F' and resid 389 through 394
    Processing helix  chain 'F' and resid 395 through 398
      removed outlier: 3.647A  pdb=" N   TRP F 398 " --> pdb=" O   GLN F 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 395 through 398'
    Processing helix  chain 'F' and resid 399 through 404
    Processing helix  chain 'F' and resid 419 through 428
      removed outlier: 3.615A  pdb=" N   ARG F 422 " --> pdb=" O   LEU F 419 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   TYR F 423 " --> pdb=" O   GLU F 420 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   LEU F 424 " --> pdb=" O   GLU F 421 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG F 425 " --> pdb=" O   ARG F 422 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLY F 427 " --> pdb=" O   LEU F 424 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP F 428 " --> pdb=" O   ARG F 425 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 444 through 452
      removed outlier: 3.806A  pdb=" N   LEU F 448 " --> pdb=" O   THR F 444 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL F 449 " --> pdb=" O   TRP F 445 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR F 450 " --> pdb=" O   LEU F 446 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE F 452 " --> pdb=" O   LEU F 448 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 459 through 470
      removed outlier: 3.888A  pdb=" N   MET F 465 " --> pdb=" O   SER F 461 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASN F 470 " --> pdb=" O   TYR F 466 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 489 through 497
      removed outlier: 3.792A  pdb=" N   TRP F 493 " --> pdb=" O   ALA F 489 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 498 through 515
      removed outlier: 3.988A  pdb=" N   VAL F 502 " --> pdb=" O   LEU F 498 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA F 503 " --> pdb=" O   GLY F 499 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLN F 507 " --> pdb=" O   ALA F 503 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR F 511 " --> pdb=" O   GLN F 507 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 525 through 551
      removed outlier: 3.804A  pdb=" N   SER F 529 " --> pdb=" O   ALA F 525 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TRP F 533 " --> pdb=" O   SER F 529 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   PHE F 534 " --> pdb=" O   ARG F 530 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE F 537 " --> pdb=" O   TRP F 533 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE F 538 " --> pdb=" O   PHE F 534 " (cutoff:3.500A)
      Proline residue:  F 545  - end of helix
      removed outlier: 3.634A  pdb=" N   PHE F 548 " --> pdb=" O   GLY F 544 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA F 551 " --> pdb=" O   ILE F 547 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 559 through 581
      removed outlier: 3.608A  pdb=" N   HIS F 563 " --> pdb=" O   SER F 559 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL F 564 " --> pdb=" O   THR F 560 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL F 565 " --> pdb=" O   ALA F 561 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA F 566 " --> pdb=" O   ALA F 562 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET F 569 " --> pdb=" O   VAL F 565 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE F 570 " --> pdb=" O   ALA F 566 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE F 571 " --> pdb=" O   ALA F 567 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL F 574 " --> pdb=" O   PHE F 570 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA F 575 " --> pdb=" O   PHE F 571 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE F 577 " --> pdb=" O   ALA F 573 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 584 through 588
      removed outlier: 4.080A  pdb=" N   LEU F 588 " --> pdb=" O   LEU F 585 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 616 through 636
      removed outlier: 4.103A  pdb=" N   TYR F 622 " --> pdb=" O   ARG F 618 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU F 623 " --> pdb=" O   TRP F 619 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL F 624 " --> pdb=" O   MET F 620 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   TRP F 625 " --> pdb=" O   SER F 621 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 641 through 644
    Processing helix  chain 'F' and resid 645 through 652
      removed outlier: 3.600A  pdb=" N   ARG F 649 " --> pdb=" O   ARG F 645 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 671 through 683
      removed outlier: 3.924A  pdb=" N   ILE F 675 " --> pdb=" O   VAL F 671 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 686 through 711
      removed outlier: 3.910A  pdb=" N   LEU F 690 " --> pdb=" O   ILE F 686 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ASP F 691 " --> pdb=" O   LEU F 687 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   THR F 692 " --> pdb=" O   PHE F 688 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   TYR F 693 " --> pdb=" O   PHE F 689 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE F 697 " --> pdb=" O   TYR F 693 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE F 698 " --> pdb=" O   LEU F 694 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   PHE F 703 " --> pdb=" O   VAL F 699 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER F 704 " --> pdb=" O   ASN F 700 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 718 through 723
      removed outlier: 3.855A  pdb=" N   ILE F 722 " --> pdb=" O   PRO F 718 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   PHE F 723 " --> pdb=" O   TRP F 719 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 718 through 723'
    Processing helix  chain 'F' and resid 726 through 734
      removed outlier: 3.578A  pdb=" N   SER F 732 " --> pdb=" O   LYS F 728 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 747 through 764
      removed outlier: 3.632A  pdb=" N   MET F 761 " --> pdb=" O   ILE F 757 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 768 through 773
      removed outlier: 3.952A  pdb=" N   GLN F 773 " --> pdb=" O   ILE F 769 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 793 through 797
    Processing helix  chain 'F' and resid 813 through 825
    Processing helix  chain 'F' and resid 857 through 862
      removed outlier: 3.938A  pdb=" N   ILE F 861 " --> pdb=" O   LEU F 857 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 871 through 880
    Processing helix  chain 'F' and resid 882 through 896
    Processing helix  chain 'F' and resid 933 through 946
      removed outlier: 3.581A  pdb=" N   ARG F 946 " --> pdb=" O   TRP F 942 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 950 through 958
    Processing helix  chain 'F' and resid 958 through 972
      removed outlier: 4.212A  pdb=" N   ARG F 962 " --> pdb=" O   MET F 958 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 973 through 979
      removed outlier: 4.328A  pdb=" N   PHE F 979 " --> pdb=" O   ILE F 975 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 982 through 995
    Processing helix  chain 'F' and resid 1006 through 1010
      removed outlier: 3.659A  pdb=" N   LYS F1009 " --> pdb=" O   ARG F1006 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1011 through 1025
      removed outlier: 3.768A  pdb=" N   GLU F1016 " --> pdb=" O   PRO F1012 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASN F1017 " --> pdb=" O   HIS F1013 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA F1018 " --> pdb=" O   GLU F1014 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU F1022 " --> pdb=" O   ALA F1018 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG F1023 " --> pdb=" O   GLU F1019 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1082 through 1089
      removed outlier: 3.950A  pdb=" N   ALA F1089 " --> pdb=" O   ASN F1085 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1109 through 1113
      removed outlier: 3.734A  pdb=" N   LEU F1113 " --> pdb=" O   GLU F1110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1114 through 1119
      removed outlier: 3.602A  pdb=" N   VAL F1118 " --> pdb=" O   LYS F1114 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU F1119 " --> pdb=" O   ILE F1115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 1114 through 1119'
    Processing helix  chain 'F' and resid 1169 through 1187
      removed outlier: 3.822A  pdb=" N   ILE F1187 " --> pdb=" O   THR F1183 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1201 through 1206
      removed outlier: 3.816A  pdb=" N   THR F1206 " --> pdb=" O   THR F1202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1223 through 1229
    Processing helix  chain 'F' and resid 1273 through 1280
      removed outlier: 3.687A  pdb=" N   TYR F1277 " --> pdb=" O   ARG F1273 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR F1280 " --> pdb=" O   TYR F1276 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1283 through 1292
    Processing helix  chain 'F' and resid 1294 through 1320
      removed outlier: 3.831A  pdb=" N   HIS F1298 " --> pdb=" O   HIS F1294 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN F1301 " --> pdb=" O   PHE F1297 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU F1302 " --> pdb=" O   HIS F1298 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE F1303 " --> pdb=" O   LEU F1299 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN F1305 " --> pdb=" O   ASN F1301 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN F1309 " --> pdb=" O   GLN F1305 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET F1310 " --> pdb=" O   LEU F1306 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   PHE F1311 " --> pdb=" O   SER F1307 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET F1312 " --> pdb=" O   LEU F1308 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU F1313 " --> pdb=" O   GLN F1309 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL F1316 " --> pdb=" O   MET F1312 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN F1317 " --> pdb=" O   LEU F1313 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1348 through 1353
    Processing helix  chain 'F' and resid 1353 through 1365
      removed outlier: 3.719A  pdb=" N   ARG F1357 " --> pdb=" O   ASP F1353 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU F1360 " --> pdb=" O   ARG F1356 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   SER F1361 " --> pdb=" O   ARG F1357 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE F1363 " --> pdb=" O   THR F1359 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE F1364 " --> pdb=" O   LEU F1360 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL F1365 " --> pdb=" O   SER F1361 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1371 through 1379
      removed outlier: 4.184A  pdb=" N   VAL F1375 " --> pdb=" O   VAL F1371 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLN F1376 " --> pdb=" O   PRO F1372 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1382 through 1393
    Processing helix  chain 'F' and resid 1398 through 1406
    Processing helix  chain 'F' and resid 1407 through 1418
      removed outlier: 3.834A  pdb=" N   SER F1411 " --> pdb=" O   GLN F1407 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1437 through 1446
      removed outlier: 3.854A  pdb=" N   PHE F1445 " --> pdb=" O   LEU F1441 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1450 through 1467
      removed outlier: 3.788A  pdb=" N   ARG F1455 " --> pdb=" O   TYR F1451 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   MET F1459 " --> pdb=" O   ARG F1455 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU F1460 " --> pdb=" O   SER F1456 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS F1467 " --> pdb=" O   GLY F1463 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1469 through 1471
      No H-bonds generated for 'chain 'F' and resid 1469 through 1471'
    Processing helix  chain 'F' and resid 1472 through 1481
      removed outlier: 3.929A  pdb=" N   TRP F1476 " --> pdb=" O   LEU F1472 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA F1477 " --> pdb=" O   LEU F1473 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER F1478 " --> pdb=" O   TRP F1474 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1497 through 1512
    Processing helix  chain 'F' and resid 1565 through 1584
      removed outlier: 3.547A  pdb=" N   TYR F1571 " --> pdb=" O   PRO F1567 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA F1572 " --> pdb=" O   CYS F1568 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS F1575 " --> pdb=" O   TYR F1571 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA F1578 " --> pdb=" O   GLY F1574 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE F1582 " --> pdb=" O   ALA F1578 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN F1583 " --> pdb=" O   PHE F1579 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1598 through 1626
      removed outlier: 4.129A  pdb=" N   ILE F1602 " --> pdb=" O   SER F1598 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE F1603 " --> pdb=" O   VAL F1599 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA F1608 " --> pdb=" O   ILE F1604 " (cutoff:3.500A)
      Proline residue:  F1609  - end of helix
    Processing helix  chain 'F' and resid 1639 through 1665
      removed outlier: 3.536A  pdb=" N   HIS F1654 " --> pdb=" O   ALA F1650 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET F1661 " --> pdb=" O   PHE F1657 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TRP F1662 " --> pdb=" O   PHE F1658 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1669 through 1697
      removed outlier: 3.937A  pdb=" N   ILE F1674 " --> pdb=" O   VAL F1670 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLY F1675 " --> pdb=" O   ARG F1671 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR F1678 " --> pdb=" O   ILE F1674 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1725 through 1751
      removed outlier: 3.802A  pdb=" N   LYS F1733 " --> pdb=" O   GLU F1729 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA F1741 " --> pdb=" O   LEU F1737 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA F1742 " --> pdb=" O   SER F1738 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY F1747 " --> pdb=" O   ASP F1743 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   HIS F1748 " --> pdb=" O   PHE F1744 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1754 through 1758
    Processing helix  chain 'F' and resid 1763 through 1775
    Processing helix  chain 'F' and resid 1786 through 1821
      removed outlier: 4.046A  pdb=" N   SER F1802 " --> pdb=" O   LYS F1798 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU F1803 " --> pdb=" O   LYS F1799 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU F1808 " --> pdb=" O   TYR F1804 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA F1809 " --> pdb=" O   PHE F1805 " (cutoff:3.500A)
      Proline residue:  F1818  - end of helix
    Processing sheet with id=AA1, first strand: chain 'F' and resid 371 through 372
    Processing sheet with id=AA2, first strand: chain 'F' and resid 779 through 781
    Processing sheet with id=AA3, first strand: chain 'F' and resid 999 through 1004
      removed outlier: 6.797A  pdb=" N   PHE F 842 " --> pdb=" O   LYS F 999 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   LEU F1001 " --> pdb=" O   PHE F 842 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   VAL F 844 " --> pdb=" O   LEU F1001 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   SER F1003 " --> pdb=" O   VAL F 844 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   THR F 846 " --> pdb=" O   SER F1003 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   THR F 843 " --> pdb=" O   GLN F1099 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ALA F1149 " --> pdb=" O   ASN F1200 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LYS F1237 " --> pdb=" O   ALA F1149 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   VAL F1151 " --> pdb=" O   LYS F1237 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   CYS F1239 " --> pdb=" O   VAL F1151 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ALA F1153 " --> pdb=" O   CYS F1239 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   TYR F1241 " --> pdb=" O   ALA F1153 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 1030 through 1032
      removed outlier: 3.878A  pdb=" N   PHE F1068 " --> pdb=" O   LEU F1051 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1458 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: 4.40

  Time building geometry restraints manager: 4.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2020
        1.32 -     1.44: 3475
        1.44 -     1.57: 7069
        1.57 -     1.69: 3
        1.69 -     1.81: 115
  Bond restraints: 12682
  Sorted by residual:
  bond pdb=" C17 XKP F1925 "
       pdb=" C22 XKP F1925 "
    ideal  model  delta    sigma   weight residual
    1.524  1.306  0.218 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" C8  XKP F1925 "
       pdb=" O2  XKP F1925 "
    ideal  model  delta    sigma   weight residual
    1.409  1.451 -0.042 2.00e-02 2.50e+03 4.51e+00
  bond pdb=" O5  XKP F1925 "
       pdb=" P   XKP F1925 "
    ideal  model  delta    sigma   weight residual
    1.647  1.606  0.041 2.00e-02 2.50e+03 4.23e+00
  bond pdb=" C3  XKP F1925 "
       pdb=" C4  XKP F1925 "
    ideal  model  delta    sigma   weight residual
    1.535  1.495  0.040 2.00e-02 2.50e+03 4.02e+00
  bond pdb=" C   LEU F 642 "
       pdb=" N   PRO F 643 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.015 8.40e-03 1.42e+04 3.33e+00
  ... (remaining 12677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 16629
        2.27 -     4.53: 422
        4.53 -     6.80: 52
        6.80 -     9.07: 10
        9.07 -    11.33: 3
  Bond angle restraints: 17116
  Sorted by residual:
  angle pdb=" N   VAL F 318 "
        pdb=" CA  VAL F 318 "
        pdb=" C   VAL F 318 "
      ideal   model   delta    sigma   weight residual
     112.90  104.78    8.12 9.60e-01 1.09e+00 7.15e+01
  angle pdb=" C   ARG F 869 "
        pdb=" CA  ARG F 869 "
        pdb=" CB  ARG F 869 "
      ideal   model   delta    sigma   weight residual
     116.54  108.36    8.18 1.15e+00 7.56e-01 5.06e+01
  angle pdb=" CA  ARG F 869 "
        pdb=" C   ARG F 869 "
        pdb=" N   VAL F 870 "
      ideal   model   delta    sigma   weight residual
     119.52  115.38    4.14 7.90e-01 1.60e+00 2.74e+01
  angle pdb=" N   ILE F 734 "
        pdb=" CA  ILE F 734 "
        pdb=" C   ILE F 734 "
      ideal   model   delta    sigma   weight residual
     113.71  109.08    4.63 9.50e-01 1.11e+00 2.37e+01
  angle pdb=" C   SER F 281 "
        pdb=" CA  SER F 281 "
        pdb=" CB  SER F 281 "
      ideal   model   delta    sigma   weight residual
     115.79  110.49    5.30 1.19e+00 7.06e-01 1.98e+01
  ... (remaining 17111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.79: 7268
       28.79 -    57.57: 308
       57.57 -    86.35: 22
       86.35 -   115.14: 3
      115.14 -   143.92: 5
  Dihedral angle restraints: 7606
    sinusoidal: 3189
      harmonic: 4417
  Sorted by residual:
  dihedral pdb=" CB  CYS F1328 "
           pdb=" SG  CYS F1328 "
           pdb=" SG  CYS F1345 "
           pdb=" CB  CYS F1345 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.43  -41.43     1      1.00e+01 1.00e-02 2.40e+01
  dihedral pdb=" CB  CYS F 658 "
           pdb=" SG  CYS F 658 "
           pdb=" SG  CYS F 669 "
           pdb=" CB  CYS F 669 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.36   40.36     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  PHE F1657 "
           pdb=" C   PHE F1657 "
           pdb=" N   PHE F1658 "
           pdb=" CA  PHE F1658 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.87   22.13     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 7603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.216: 1890
       0.216 -    0.432: 3
       0.432 -    0.649: 0
       0.649 -    0.865: 0
       0.865 -    1.081: 1
  Chirality restraints: 1894
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN F1849 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -3.48    1.08 2.00e-01 2.50e+01 2.92e+01
  chirality pdb=" C1  BGC C   3 "
            pdb=" O3  BGC C   2 "
            pdb=" C2  BGC C   3 "
            pdb=" O5  BGC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.32   -0.08 2.00e-02 2.50e+03 1.58e+01
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.19e+01
  ... (remaining 1891 not shown)

  Planarity restraints: 2123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "    0.278 2.00e-02 2.50e+03   2.33e-01 6.77e+02
        pdb=" C7  NAG A   1 "   -0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "    0.183 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "   -0.393 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "   -0.136 2.00e-02 2.50e+03   1.12e-01 1.56e+02
        pdb=" C7  NAG A   2 "    0.037 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "   -0.101 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "    0.179 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN F1849 "    0.063 2.00e-02 2.50e+03   5.99e-02 4.49e+01
        pdb=" CG  ASN F1849 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASN F1849 "   -0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN F1849 "   -0.091 2.00e-02 2.50e+03
        pdb=" C1  NAG A   1 "    0.070 2.00e-02 2.50e+03
  ... (remaining 2120 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 159
        2.64 -     3.21: 11238
        3.21 -     3.77: 16802
        3.77 -     4.34: 22815
        4.34 -     4.90: 38412
  Nonbonded interactions: 89426
  Sorted by model distance:
  nonbonded pdb=" O4  BGC C   3 "
            pdb=" O5  BGC C   4 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" O3  NAG A   2 "
            pdb=" O7  NAG A   2 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O2  BGC C   1 "
            pdb=" O2  BGC C   2 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" O   MET F 458 "
            pdb=" OH  TYR F 633 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" NH1 ARG F 344 "
            pdb=" O   GLU F 346 "
     model   vdw
     2.231 3.120
  ... (remaining 89421 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.610
  Find NCS groups from input model:        0.150
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
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      :  0.007   0.310  12689  Z= 0.337
  Angle     :  0.900  18.638  17135  Z= 0.510
  Chirality :  0.054   1.081   1894
  Planarity :  0.007   0.233   2122
  Dihedral  : 15.055 143.924   4742
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.66 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.47 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.22), residues: 1481
  helix: -0.61 (0.18), residues: 842
  sheet: -2.90 (0.69), residues: 56
  loop : -3.15 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 625 
 HIS   0.011   0.001   HIS F 384 
 PHE   0.025   0.002   PHE F 796 
 TYR   0.019   0.001   TYR F1093 
 ARG   0.005   0.000   ARG F 940 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.31008 (    1)
  link_NAG-ASN         : angle      12.68019 (    3)
  link_BETA1-4         : bond        0.00070 (    1)
  link_BETA1-4         : angle       0.32062 (    3)
  hydrogen bonds       : bond        0.19234 (  498)
  hydrogen bonds       : angle       5.90455 ( 1458)
  SS BOND              : bond        0.18712 (    2)
  SS BOND              : angle       7.08511 (    4)
  link_BETA1-3         : bond        0.03331 (    3)
  link_BETA1-3         : angle       4.13973 (    9)
  covalent geometry    : bond        0.00613 (12682)
  covalent geometry    : angle       0.87311 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 167
  time to evaluate  : 1.375 
Fit side-chains
REVERT: F  241 MET cc_start: 0.8325 (ttm) cc_final: 0.8112 (ttp)
REVERT: F  493 TRP cc_start: 0.8117 (m-10) cc_final: 0.7530 (m100)
REVERT: F 1362 ILE cc_start: 0.9253 (tp) cc_final: 0.8915 (tp)
REVERT: F 1498 ASP cc_start: 0.6231 (p0) cc_final: 0.5891 (t0)
REVERT: F 1766 PHE cc_start: 0.7364 (m-80) cc_final: 0.7065 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 169
  average time/residue: 0.2820
  time to fit residues: 67.1106
Evaluate side-chains
  132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  669 CYS
Chi-restraints excluded: chain F residue  670 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.1980
   chunk 113 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 117 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0070
   chunk 71 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 136 optimal weight:    0.0170
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
F 316 ASN
F1107 ASN
F1238 HIS
** F1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1859 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.157389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.098490 restraints weight = 18026.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101094 restraints weight = 12123.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.102421 restraints weight = 10100.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12689  Z= 0.126
  Angle     :  0.633   6.578  17135  Z= 0.317
  Chirality :  0.042   0.172   1894
  Planarity :  0.004   0.051   2122
  Dihedral  :  9.276 120.900   1959
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.98 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.64 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.22), residues: 1481
  helix:  0.00 (0.19), residues: 840
  sheet: -2.03 (0.81), residues: 49
  loop : -3.07 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 625 
 HIS   0.007   0.001   HIS F1238 
 PHE   0.013   0.001   PHE F 796 
 TYR   0.019   0.001   TYR F 875 
 ARG   0.004   0.000   ARG F 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01165 (    1)
  link_NAG-ASN         : angle       3.69482 (    3)
  link_BETA1-4         : bond        0.01251 (    1)
  link_BETA1-4         : angle       1.48612 (    3)
  hydrogen bonds       : bond        0.05099 (  498)
  hydrogen bonds       : angle       4.16529 ( 1458)
  SS BOND              : bond        0.00411 (    2)
  SS BOND              : angle       1.23355 (    4)
  link_BETA1-3         : bond        0.00170 (    3)
  link_BETA1-3         : angle       3.29692 (    9)
  covalent geometry    : bond        0.00263 (12682)
  covalent geometry    : angle       0.62622 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 1.289 
Fit side-chains
REVERT: F  241 MET cc_start: 0.8272 (ttm) cc_final: 0.8052 (ttt)
REVERT: F  493 TRP cc_start: 0.8115 (m-10) cc_final: 0.7429 (m100)
REVERT: F  978 MET cc_start: 0.7064 (mmt) cc_final: 0.6860 (mmt)
REVERT: F 1362 ILE cc_start: 0.9153 (tp) cc_final: 0.8919 (tp)
REVERT: F 1444 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.8109 (ttp80)
REVERT: F 1498 ASP cc_start: 0.6095 (p0) cc_final: 0.5893 (t0)
REVERT: F 1610 ILE cc_start: 0.8534 (mm) cc_final: 0.8303 (mt)
  outliers start: 10
  outliers final: 4
  residues processed: 156
  average time/residue: 0.2763
  time to fit residues: 61.2622
Evaluate side-chains
  137 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue 1084 ASP
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1749 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 92 optimal weight:   40.0000
   chunk 77 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 132 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 133 optimal weight:    1.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
F1088 HIS
F1107 ASN
** F1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1647 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.156148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.097063 restraints weight = 18138.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099653 restraints weight = 12207.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.100738 restraints weight = 10195.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12689  Z= 0.135
  Angle     :  0.608   9.798  17135  Z= 0.301
  Chirality :  0.042   0.171   1894
  Planarity :  0.004   0.034   2122
  Dihedral  :  8.163 106.704   1954
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.59 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.35 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.22), residues: 1481
  helix:  0.21 (0.19), residues: 851
  sheet: -1.88 (0.82), residues: 49
  loop : -2.99 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 625 
 HIS   0.005   0.001   HIS F 384 
 PHE   0.020   0.001   PHE F1766 
 TYR   0.015   0.001   TYR F1330 
 ARG   0.006   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00062 (    1)
  link_NAG-ASN         : angle       3.35665 (    3)
  link_BETA1-4         : bond        0.00471 (    1)
  link_BETA1-4         : angle       2.28866 (    3)
  hydrogen bonds       : bond        0.04695 (  498)
  hydrogen bonds       : angle       3.88162 ( 1458)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       0.95398 (    4)
  link_BETA1-3         : bond        0.00284 (    3)
  link_BETA1-3         : angle       3.07076 (    9)
  covalent geometry    : bond        0.00314 (12682)
  covalent geometry    : angle       0.60201 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.589 
Fit side-chains
REVERT: F  493 TRP cc_start: 0.8142 (m-10) cc_final: 0.7457 (m100)
REVERT: F 1346 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6786 (p90)
REVERT: F 1498 ASP cc_start: 0.6131 (p0) cc_final: 0.5861 (t0)
REVERT: F 1610 ILE cc_start: 0.8515 (mm) cc_final: 0.8261 (mt)
REVERT: F 1729 GLU cc_start: 0.7425 (pp20) cc_final: 0.6955 (tm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 155
  average time/residue: 0.2768
  time to fit residues: 61.2480
Evaluate side-chains
  143 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  438 THR
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue 1084 ASP
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1691 THR
Chi-restraints excluded: chain F residue 1749 VAL
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 110 optimal weight:    0.7980
   chunk 77 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 139 optimal weight:    0.8980
   chunk 138 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 142 optimal weight:    0.0370
   chunk 116 optimal weight:    0.9980
   overall best weight:    1.5460

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

Flipped N/Q/H residues before XYZ refinement:
F 779 GLN
F1107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.156481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.097152 restraints weight = 18113.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099741 restraints weight = 12244.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.101032 restraints weight = 10249.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12689  Z= 0.129
  Angle     :  0.600  14.885  17135  Z= 0.294
  Chirality :  0.042   0.171   1894
  Planarity :  0.003   0.039   2122
  Dihedral  :  7.439 100.307   1954
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.98 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.55 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.23), residues: 1481
  helix:  0.44 (0.19), residues: 846
  sheet: -1.74 (0.82), residues: 49
  loop : -2.93 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 625 
 HIS   0.005   0.001   HIS F1647 
 PHE   0.019   0.001   PHE F1766 
 TYR   0.015   0.001   TYR F1330 
 ARG   0.008   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       2.80852 (    3)
  link_BETA1-4         : bond        0.00368 (    1)
  link_BETA1-4         : angle       2.71050 (    3)
  hydrogen bonds       : bond        0.04259 (  498)
  hydrogen bonds       : angle       3.70319 ( 1458)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       0.90582 (    4)
  link_BETA1-3         : bond        0.00179 (    3)
  link_BETA1-3         : angle       2.95288 (    9)
  covalent geometry    : bond        0.00299 (12682)
  covalent geometry    : angle       0.59404 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.947 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: F  348 MET cc_start: 0.8883 (mtt) cc_final: 0.8652 (mtt)
REVERT: F  493 TRP cc_start: 0.8093 (m-10) cc_final: 0.7395 (m100)
REVERT: F  957 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8961 (t80)
REVERT: F 1346 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.6891 (p90)
REVERT: F 1610 ILE cc_start: 0.8543 (mm) cc_final: 0.8275 (mt)
REVERT: F 1729 GLU cc_start: 0.7510 (pp20) cc_final: 0.7058 (tm-30)
  outliers start: 30
  outliers final: 19
  residues processed: 160
  average time/residue: 0.3558
  time to fit residues: 83.0498
Evaluate side-chains
  152 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  387 ILE
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  438 THR
Chi-restraints excluded: chain F residue  526 GLN
Chi-restraints excluded: chain F residue  541 ILE
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1015 LEU
Chi-restraints excluded: chain F residue 1084 ASP
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1691 THR
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 144 optimal weight:    0.8980
   chunk 138 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 128 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 139 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.156638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.097712 restraints weight = 18045.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.100236 restraints weight = 12130.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.101589 restraints weight = 10154.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12689  Z= 0.123
  Angle     :  0.583  11.765  17135  Z= 0.286
  Chirality :  0.041   0.168   1894
  Planarity :  0.003   0.036   2122
  Dihedral  :  7.056  99.155   1954
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.25 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.81 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.23), residues: 1481
  helix:  0.58 (0.19), residues: 846
  sheet: -1.24 (0.85), residues: 48
  loop : -2.87 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 625 
 HIS   0.005   0.001   HIS F1647 
 PHE   0.017   0.001   PHE F1766 
 TYR   0.015   0.001   TYR F1330 
 ARG   0.007   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       2.58391 (    3)
  link_BETA1-4         : bond        0.00289 (    1)
  link_BETA1-4         : angle       2.91811 (    3)
  hydrogen bonds       : bond        0.04079 (  498)
  hydrogen bonds       : angle       3.58651 ( 1458)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       0.85593 (    4)
  link_BETA1-3         : bond        0.00186 (    3)
  link_BETA1-3         : angle       2.91136 (    9)
  covalent geometry    : bond        0.00285 (12682)
  covalent geometry    : angle       0.57696 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8619 (pp)
REVERT: F  348 MET cc_start: 0.8892 (mtt) cc_final: 0.8655 (mtt)
REVERT: F  493 TRP cc_start: 0.8095 (m-10) cc_final: 0.7401 (m100)
REVERT: F  957 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8900 (t80)
REVERT: F 1346 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.6958 (p90)
REVERT: F 1610 ILE cc_start: 0.8550 (mm) cc_final: 0.8264 (mt)
REVERT: F 1729 GLU cc_start: 0.7484 (pp20) cc_final: 0.7004 (tm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 162
  average time/residue: 0.2748
  time to fit residues: 63.0578
Evaluate side-chains
  155 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  387 ILE
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  438 THR
Chi-restraints excluded: chain F residue  541 ILE
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  795 PHE
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1084 ASP
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1689 CYS
Chi-restraints excluded: chain F residue 1691 THR
Chi-restraints excluded: chain F residue 1749 VAL
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 32 optimal weight:    0.0060
   chunk 65 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 90 optimal weight:    0.4980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.158431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.099871 restraints weight = 18257.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.102524 restraints weight = 12119.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.103884 restraints weight = 10088.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12689  Z= 0.099
  Angle     :  0.553  10.365  17135  Z= 0.272
  Chirality :  0.040   0.171   1894
  Planarity :  0.003   0.036   2122
  Dihedral  :  6.638  96.216   1954
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.51 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.31 %
    Favored  : 81.56 %
  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: -0.92 (0.23), residues: 1481
  helix:  0.77 (0.19), residues: 851
  sheet: -0.30 (1.01), residues: 39
  loop : -2.83 (0.24), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 625 
 HIS   0.004   0.001   HIS F1088 
 PHE   0.030   0.001   PHE F 887 
 TYR   0.014   0.001   TYR F1330 
 ARG   0.007   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00130 (    1)
  link_NAG-ASN         : angle       2.35904 (    3)
  link_BETA1-4         : bond        0.00435 (    1)
  link_BETA1-4         : angle       2.96125 (    3)
  hydrogen bonds       : bond        0.03403 (  498)
  hydrogen bonds       : angle       3.42607 ( 1458)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       0.78679 (    4)
  link_BETA1-3         : bond        0.00201 (    3)
  link_BETA1-3         : angle       2.86875 (    9)
  covalent geometry    : bond        0.00211 (12682)
  covalent geometry    : angle       0.54666 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8599 (pp)
REVERT: F  348 MET cc_start: 0.8848 (mtt) cc_final: 0.8607 (mtt)
REVERT: F  493 TRP cc_start: 0.8125 (m-10) cc_final: 0.7431 (m100)
REVERT: F  526 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7747 (mt0)
REVERT: F  816 GLU cc_start: 0.7966 (tt0) cc_final: 0.7509 (tt0)
REVERT: F  957 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (t80)
REVERT: F 1019 GLU cc_start: 0.8648 (tp30) cc_final: 0.8433 (tp30)
REVERT: F 1346 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.6833 (p90)
REVERT: F 1610 ILE cc_start: 0.8503 (mm) cc_final: 0.8208 (mt)
REVERT: F 1729 GLU cc_start: 0.7505 (pp20) cc_final: 0.6964 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 164
  average time/residue: 0.2910
  time to fit residues: 68.1344
Evaluate side-chains
  151 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  444 THR
Chi-restraints excluded: chain F residue  526 GLN
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  795 PHE
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1148 VAL
Chi-restraints excluded: chain F residue 1341 VAL
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1806 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 144 optimal weight:    2.9990
   chunk 142 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 137 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0270
   chunk 124 optimal weight:    0.0000
   chunk 114 optimal weight:    0.1980
   chunk 140 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.2842

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.161854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.107453 restraints weight = 18300.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.106068 restraints weight = 13135.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.105841 restraints weight = 11655.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12689  Z= 0.096
  Angle     :  0.541   9.736  17135  Z= 0.266
  Chirality :  0.040   0.202   1894
  Planarity :  0.003   0.036   2122
  Dihedral  :  6.192  95.904   1954
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.10 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.49 %
    Favored  : 80.85 %
  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: -0.67 (0.23), residues: 1481
  helix:  0.99 (0.19), residues: 856
  sheet: -0.16 (1.01), residues: 39
  loop : -2.77 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F1468 
 HIS   0.005   0.001   HIS F 384 
 PHE   0.015   0.001   PHE F 548 
 TYR   0.015   0.001   TYR F1330 
 ARG   0.007   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    1)
  link_NAG-ASN         : angle       2.29837 (    3)
  link_BETA1-4         : bond        0.00407 (    1)
  link_BETA1-4         : angle       2.91954 (    3)
  hydrogen bonds       : bond        0.03066 (  498)
  hydrogen bonds       : angle       3.32591 ( 1458)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       0.74500 (    4)
  link_BETA1-3         : bond        0.00182 (    3)
  link_BETA1-3         : angle       2.82540 (    9)
  covalent geometry    : bond        0.00200 (12682)
  covalent geometry    : angle       0.53474 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 1.516 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8510 (pp)
REVERT: F  493 TRP cc_start: 0.8079 (m-10) cc_final: 0.7377 (m100)
REVERT: F  816 GLU cc_start: 0.8003 (tt0) cc_final: 0.7509 (tt0)
REVERT: F 1019 GLU cc_start: 0.8666 (tp30) cc_final: 0.8434 (tp30)
REVERT: F 1346 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.6674 (p90)
REVERT: F 1478 SER cc_start: 0.8941 (m) cc_final: 0.8695 (t)
REVERT: F 1610 ILE cc_start: 0.8428 (mm) cc_final: 0.8136 (mt)
  outliers start: 21
  outliers final: 14
  residues processed: 157
  average time/residue: 0.3466
  time to fit residues: 77.3577
Evaluate side-chains
  152 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  432 ASP
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  795 PHE
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1148 VAL
Chi-restraints excluded: chain F residue 1341 VAL
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1730 LEU
Chi-restraints excluded: chain F residue 1806 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 144 optimal weight:   10.0000
   chunk 133 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0030
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.9596

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

Flipped N/Q/H residues before XYZ refinement:
F 526 GLN
F 765 HIS
F1107 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.156143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.101954 restraints weight = 18159.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.100803 restraints weight = 12552.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.099926 restraints weight = 11515.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12689  Z= 0.148
  Angle     :  0.597  14.868  17135  Z= 0.293
  Chirality :  0.042   0.205   1894
  Planarity :  0.003   0.039   2122
  Dihedral  :  6.477 102.634   1954
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.78 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.05 %
    Favored  : 79.91 %
  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: -0.63 (0.23), residues: 1481
  helix:  1.01 (0.19), residues: 856
  sheet:  0.06 (1.01), residues: 38
  loop : -2.74 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 625 
 HIS   0.007   0.001   HIS F 765 
 PHE   0.017   0.001   PHE F1766 
 TYR   0.029   0.001   TYR F1093 
 ARG   0.008   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       2.44519 (    3)
  link_BETA1-4         : bond        0.00149 (    1)
  link_BETA1-4         : angle       3.02715 (    3)
  hydrogen bonds       : bond        0.04035 (  498)
  hydrogen bonds       : angle       3.44986 ( 1458)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       0.75624 (    4)
  link_BETA1-3         : bond        0.00163 (    3)
  link_BETA1-3         : angle       2.78723 (    9)
  covalent geometry    : bond        0.00352 (12682)
  covalent geometry    : angle       0.59179 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8569 (pp)
REVERT: F  348 MET cc_start: 0.9021 (mtt) cc_final: 0.8764 (mtt)
REVERT: F  493 TRP cc_start: 0.8151 (m-10) cc_final: 0.7420 (m100)
REVERT: F  957 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8803 (t80)
REVERT: F 1346 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.6905 (p90)
REVERT: F 1610 ILE cc_start: 0.8488 (mm) cc_final: 0.8183 (mt)
REVERT: F 1642 MET cc_start: 0.4463 (ttt) cc_final: 0.4171 (ttt)
REVERT: F 1729 GLU cc_start: 0.7488 (pp20) cc_final: 0.6913 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 158
  average time/residue: 0.3071
  time to fit residues: 70.2107
Evaluate side-chains
  155 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  432 ASP
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1100 LEU
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1148 VAL
Chi-restraints excluded: chain F residue 1341 VAL
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1730 LEU
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Chi-restraints excluded: chain F residue 1855 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0970
   chunk 138 optimal weight:    8.9990
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.156598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.097761 restraints weight = 17996.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.101022 restraints weight = 12813.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.100634 restraints weight = 9818.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12689  Z= 0.126
  Angle     :  0.591  14.933  17135  Z= 0.288
  Chirality :  0.042   0.198   1894
  Planarity :  0.003   0.041   2122
  Dihedral  :  6.465 101.704   1954
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.17 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.44 %
    Favored  : 79.59 %
  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: -0.57 (0.23), residues: 1481
  helix:  1.07 (0.19), residues: 856
  sheet:  0.07 (1.01), residues: 38
  loop : -2.73 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 625 
 HIS   0.005   0.001   HIS F 384 
 PHE   0.016   0.001   PHE F1766 
 TYR   0.026   0.001   TYR F1093 
 ARG   0.010   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       2.35364 (    3)
  link_BETA1-4         : bond        0.00206 (    1)
  link_BETA1-4         : angle       3.16081 (    3)
  hydrogen bonds       : bond        0.03803 (  498)
  hydrogen bonds       : angle       3.42662 ( 1458)
  SS BOND              : bond        0.00279 (    2)
  SS BOND              : angle       0.73178 (    4)
  link_BETA1-3         : bond        0.00139 (    3)
  link_BETA1-3         : angle       2.76535 (    9)
  covalent geometry    : bond        0.00295 (12682)
  covalent geometry    : angle       0.58541 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
REVERT: F  230 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8562 (pp)
REVERT: F  493 TRP cc_start: 0.8150 (m-10) cc_final: 0.7389 (m100)
REVERT: F  957 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8836 (t80)
REVERT: F 1019 GLU cc_start: 0.8699 (tp30) cc_final: 0.8442 (tp30)
REVERT: F 1346 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.6911 (p90)
REVERT: F 1610 ILE cc_start: 0.8454 (mm) cc_final: 0.8153 (mt)
REVERT: F 1642 MET cc_start: 0.4548 (ttt) cc_final: 0.4257 (ttt)
REVERT: F 1729 GLU cc_start: 0.7490 (pp20) cc_final: 0.6899 (tm-30)
  outliers start: 25
  outliers final: 22
  residues processed: 152
  average time/residue: 0.3723
  time to fit residues: 81.6282
Evaluate side-chains
  159 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 2.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  432 ASP
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  795 PHE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1148 VAL
Chi-restraints excluded: chain F residue 1341 VAL
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1365 VAL
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1596 VAL
Chi-restraints excluded: chain F residue 1730 LEU
Chi-restraints excluded: chain F residue 1750 ILE
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Chi-restraints excluded: chain F residue 1815 ILE
Chi-restraints excluded: chain F residue 1855 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 148 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0870
   chunk 113 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    2.4164

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.096378 restraints weight = 18121.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.098802 restraints weight = 12426.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.100149 restraints weight = 10470.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12689  Z= 0.171
  Angle     :  0.622  15.228  17135  Z= 0.306
  Chirality :  0.043   0.205   1894
  Planarity :  0.004   0.045   2122
  Dihedral  :  6.822 105.239   1954
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.78 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.20 %
    Favored  : 79.67 %
  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: -0.62 (0.23), residues: 1481
  helix:  1.01 (0.19), residues: 858
  sheet:  0.01 (1.01), residues: 38
  loop : -2.75 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 625 
 HIS   0.005   0.001   HIS F 384 
 PHE   0.025   0.002   PHE F 887 
 TYR   0.024   0.001   TYR F1093 
 ARG   0.010   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       2.35908 (    3)
  link_BETA1-4         : bond        0.00005 (    1)
  link_BETA1-4         : angle       3.34855 (    3)
  hydrogen bonds       : bond        0.04378 (  498)
  hydrogen bonds       : angle       3.55011 ( 1458)
  SS BOND              : bond        0.00401 (    2)
  SS BOND              : angle       0.74885 (    4)
  link_BETA1-3         : bond        0.00169 (    3)
  link_BETA1-3         : angle       2.73171 (    9)
  covalent geometry    : bond        0.00411 (12682)
  covalent geometry    : angle       0.61665 (17116)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 1.271 
Fit side-chains
REVERT: F  230 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8594 (pp)
REVERT: F  493 TRP cc_start: 0.8178 (m-10) cc_final: 0.7408 (m100)
REVERT: F  957 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8794 (t80)
REVERT: F 1346 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7026 (p90)
REVERT: F 1610 ILE cc_start: 0.8547 (mm) cc_final: 0.8237 (mt)
REVERT: F 1642 MET cc_start: 0.4490 (ttt) cc_final: 0.4201 (ttt)
REVERT: F 1729 GLU cc_start: 0.7548 (pp20) cc_final: 0.6898 (tm-30)
  outliers start: 27
  outliers final: 21
  residues processed: 158
  average time/residue: 0.2710
  time to fit residues: 60.6496
Evaluate side-chains
  159 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  430 VAL
Chi-restraints excluded: chain F residue  432 ASP
Chi-restraints excluded: chain F residue  444 THR
Chi-restraints excluded: chain F residue  776 LEU
Chi-restraints excluded: chain F residue  795 PHE
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  846 THR
Chi-restraints excluded: chain F residue  936 THR
Chi-restraints excluded: chain F residue  957 PHE
Chi-restraints excluded: chain F residue 1100 LEU
Chi-restraints excluded: chain F residue 1130 VAL
Chi-restraints excluded: chain F residue 1144 THR
Chi-restraints excluded: chain F residue 1148 VAL
Chi-restraints excluded: chain F residue 1341 VAL
Chi-restraints excluded: chain F residue 1346 TYR
Chi-restraints excluded: chain F residue 1365 VAL
Chi-restraints excluded: chain F residue 1371 VAL
Chi-restraints excluded: chain F residue 1374 VAL
Chi-restraints excluded: chain F residue 1730 LEU
Chi-restraints excluded: chain F residue 1773 TRP
Chi-restraints excluded: chain F residue 1806 LEU
Chi-restraints excluded: chain F residue 1855 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 133 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 142 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
F1107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.096935 restraints weight = 17973.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.099424 restraints weight = 12125.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.100833 restraints weight = 10139.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12689  Z= 0.133
  Angle     :  0.606  16.085  17135  Z= 0.296
  Chirality :  0.042   0.192   1894
  Planarity :  0.003   0.044   2122
  Dihedral  :  6.697 103.443   1954
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.31 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.75 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.23), residues: 1481
  helix:  1.16 (0.19), residues: 847
  sheet:  0.06 (1.01), residues: 38
  loop : -2.70 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 625 
 HIS   0.006   0.001   HIS F 384 
 PHE   0.018   0.001   PHE F1766 
 TYR   0.025   0.001   TYR F1093 
 ARG   0.009   0.000   ARG F1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00148 (    1)
  link_NAG-ASN         : angle       2.29100 (    3)
  link_BETA1-4         : bond        0.00115 (    1)
  link_BETA1-4         : angle       3.41559 (    3)
  hydrogen bonds       : bond        0.03988 (  498)
  hydrogen bonds       : angle       3.48289 ( 1458)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       0.73398 (    4)
  link_BETA1-3         : bond        0.00169 (    3)
  link_BETA1-3         : angle       2.70979 (    9)
  covalent geometry    : bond        0.00311 (12682)
  covalent geometry    : angle       0.60074 (17116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4534.51 seconds
wall clock time: 82 minutes 4.34 seconds (4924.34 seconds total)