Starting phenix.real_space_refine
on Wed Mar  4 10:56:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nxd_12637/03_2026/7nxd_12637.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      7      9.91       5
     Mg      1      5.21       5
     S      94      5.16       5
     C    7948      2.51       5
     N    2142      2.21       5
     O    2613      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12805
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 6953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 905, 6953
          Classifications: {'peptide': 905}
          Link IDs: {'PTRANS': 58, 'TRANS': 846}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 690, 5314
          Classifications: {'peptide': 690}
          Link IDs: {'PTRANS': 25, 'TRANS': 664}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          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: 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: "G"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 75
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "H"
      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: "I"
      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: "J"
      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: "K"
      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: "L"
      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: "M"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "N"
      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: "O"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "P"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 19
          Unusual residues: {' CA': 5, 'NAG': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 28
    residue:
      pdb=" N   ALA A 784 " occ=0.66
      ... (3 atoms not shown)
      pdb=" CB  ALA A 784 " occ=0.66
    residue:
      pdb=" N   TYR A 789 " occ=0.66
      ... (10 atoms not shown)
      pdb=" OH  TYR A 789 " occ=0.66
    residue:
      pdb=" N   GLU A 790 " occ=0.66
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 790 " occ=0.66
    residue:
      pdb=" N   LEU A 882 " occ=0.66
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 882 " occ=0.66
    residue:
      pdb=" N   TRP A 900 " occ=0.66
      ... (12 atoms not shown)
      pdb=" CH2 TRP A 900 " occ=0.66
    residue:
      pdb=" N   PRO A 926 " occ=0.66
      ... (5 atoms not shown)
      pdb=" CD  PRO A 926 " occ=0.66
    residue:
      pdb=" N   TYR A 927 " occ=0.66
      ... (10 atoms not shown)
      pdb=" OH  TYR A 927 " occ=0.66
    residue:
      pdb=" N   GLY B 618 " occ=0.75
      ... (2 atoms not shown)
      pdb=" O   GLY B 618 " occ=0.75
    residue:
      pdb=" N   CYS B 620 " occ=0.75
      ... (4 atoms not shown)
      pdb=" SG  CYS B 620 " occ=0.75
    residue:
      pdb=" N   LYS B 624 " occ=0.75
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 624 " occ=0.75
    residue:
      pdb=" N   GLU B 625 " occ=0.75
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 625 " occ=0.75
    residue:
      pdb=" N   CYS B 626 " occ=0.75
      ... (4 atoms not shown)
      pdb=" SG  CYS B 626 " occ=0.75
    ... (remaining 16 not shown)
  Time building chain proxies: 2.89, per 1000 atoms: 0.23
  Number of scatterers: 12805
  At special positions: 0
  Unit cell: (104.55, 136, 168.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      7     19.99
     S      94     16.00
     Mg      1     11.99
     O    2613      8.00
     N    2142      7.00
     C    7948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=37, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  58 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 472 " - pdb=" SG  CYS A 481 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 487 " - pdb=" SG  CYS A 543 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 604 " - pdb=" SG  CYS A 610 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 677 " - pdb=" SG  CYS A 690 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 808 " - pdb=" SG  CYS A 916 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 828 " - pdb=" SG  CYS A 880 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 870 " - pdb=" SG  CYS A 875 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  25 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 444 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  18 " - pdb=" SG  CYS B  44 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 187 " - pdb=" SG  CYS B 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 281 " distance=1.83
    Simple disulfide: pdb=" SG  CYS B 381 " - pdb=" SG  CYS B 395 " distance=2.30
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 442 " distance=1.92
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 457 " - pdb=" SG  CYS B 469 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 482 " - pdb=" SG  CYS B 513 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 496 " - pdb=" SG  CYS B 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 505 " - pdb=" SG  CYS B 516 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 518 " - pdb=" SG  CYS B 533 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 535 " - pdb=" SG  CYS B 556 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 540 " - pdb=" SG  CYS B 554 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 548 " - pdb=" SG  CYS B 559 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 561 " - pdb=" SG  CYS B 570 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 572 " - pdb=" SG  CYS B 595 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 579 " - pdb=" SG  CYS B 593 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 587 " - pdb=" SG  CYS B 598 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 600 " - pdb=" SG  CYS B 610 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 613 " - pdb=" SG  CYS B 616 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 620 " - pdb=" SG  CYS B 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 626 " - pdb=" SG  CYS B 645 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 629 " - pdb=" SG  CYS B 641 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 679 " - pdb=" SG  CYS B 703 " 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
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " BMA G   3 " - " MAN G   6 "
    ALPHA1-6
      " BMA G   3 " - " MAN G   4 "
    BETA1-2
      " MAN G   4 " - " NAG G   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG L   1 " - " NAG L   2 "
      " NAG M   1 " - " NAG M   2 "
      " NAG M   2 " - " BMA M   3 "
      " NAG N   1 " - " NAG N   2 "
      " NAG O   1 " - " NAG O   2 "
      " NAG O   2 " - " BMA O   3 "
      " NAG P   1 " - " NAG P   2 "
      " NAG P   2 " - " BMA P   3 "
    NAG-ASN
      " NAG A1106 " - " ASN A 483 "
      " NAG C   1 " - " ASN A  43 "
      " NAG D   1 " - " ASN A 141 "
      " NAG E   1 " - " ASN A 256 "
      " NAG F   1 " - " ASN A 266 "
      " NAG G   1 " - " ASN A 275 "
      " NAG H   1 " - " ASN A 568 "
      " NAG I   1 " - " ASN A 489 "
      " NAG J   1 " - " ASN B 192 "
      " NAG K   1 " - " ASN B 249 "
      " NAG L   1 " - " ASN B 343 "
      " NAG M   1 " - " ASN B 386 "
      " NAG N   1 " - " ASN B 397 "
      " NAG O   1 " - " ASN B 461 "
      " NAG P   1 " - " ASN B  30 "
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 655.0 milliseconds
  

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2900

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 29 sheets defined
      12.9% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 80 through 87
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 196 through 204
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 254 through 259
    Processing helix  chain 'A' and resid 509 through 512
    Processing helix  chain 'A' and resid 869 through 873
    Processing helix  chain 'A' and resid 900 through 907
      removed outlier: 3.731A  pdb=" N   ARG A 907 " --> pdb=" O   THR A 903 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 14 through 22
      removed outlier: 3.702A  pdb=" N   CYS B  18 " --> pdb=" O   SER B  14 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B  19 " --> pdb=" O   CYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 42
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.590A  pdb=" N   GLY B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 135 through 157
      removed outlier: 3.509A  pdb=" N   ASN B 141 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER B 144 " --> pdb=" O   GLU B 140 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   THR B 147 " --> pdb=" O   LYS B 143 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASN B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG B 155 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 185
      removed outlier: 3.813A  pdb=" N   ASN B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 219
      removed outlier: 4.040A  pdb=" N   PHE B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 242
      removed outlier: 3.705A  pdb=" N   ALA B 234 " --> pdb=" O   GLY B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
    Processing helix  chain 'B' and resid 321 through 332
      removed outlier: 3.834A  pdb=" N   ASN B 330 " --> pdb=" O   LYS B 326 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 361
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 444 through 450
    Processing helix  chain 'B' and resid 503 through 507
    Processing helix  chain 'B' and resid 546 through 551
      removed outlier: 3.503A  pdb=" N   GLY B 549 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 623
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 3.728A  pdb=" N   SER A 437 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 418 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
      removed outlier: 4.025A  pdb=" N   TYR A  26 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER A  34 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   VAL A  55 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95
      removed outlier: 4.093A  pdb=" N   SER A 120 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108
      removed outlier: 4.061A  pdb=" N   THR A 139 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG A 144 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172
      removed outlier: 3.580A  pdb=" N   SER A 169 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 217 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238
      removed outlier: 4.106A  pdb=" N   SER A 234 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR A 274 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASN A 266 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 272 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 288 through 292
      removed outlier: 3.578A  pdb=" N   ALA A 288 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   VAL A 326 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU A 340 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312
      removed outlier: 3.637A  pdb=" N   GLN A 319 " --> pdb=" O   ASP A 311 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 357
      removed outlier: 3.780A  pdb=" N   VAL A 369 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   VAL A 384 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU A 402 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A 386 " --> pdb=" O   GLN A 400 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521
      removed outlier: 3.510A  pdb=" N   LEU A 488 " --> pdb=" O   ASP A 542 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 544 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   PHE A 486 " --> pdb=" O   ARG A 544 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   SER A 485 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 459 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN A 489 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER A 491 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 498 through 499
    Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 532
    Processing sheet with id=AB4, first strand: chain 'A' and resid 529 through 532
    Processing sheet with id=AB5, first strand: chain 'A' and resid 614 through 621
      removed outlier: 3.555A  pdb=" N   GLU A 621 " --> pdb=" O   ASN A 634 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ASN A 634 " --> pdb=" O   GLU A 621 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 664 " --> pdb=" O   ARG A 707 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   THR A 709 " --> pdb=" O   TYR A 662 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   TYR A 662 " --> pdb=" O   THR A 709 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 677 through 680
      removed outlier: 3.743A  pdb=" N   LEU A 687 " --> pdb=" O   PHE A 680 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 688 " --> pdb=" O   VAL A 654 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   ALA A 650 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN A 725 " --> pdb=" O   ARG A 653 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A 723 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 751 through 757
      removed outlier: 6.304A  pdb=" N   GLN A 894 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL A 823 " --> pdb=" O   GLN A 894 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   HIS A 896 " --> pdb=" O   THR A 821 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 828 through 830
      removed outlier: 3.655A  pdb=" N   LEU A 804 " --> pdb=" O   CYS A 880 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   GLN A 801 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 923 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   GLN A 866 " --> pdb=" O   SER A 913 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   GLN A 915 " --> pdb=" O   GLN A 866 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LEU A 868 " --> pdb=" O   GLN A 915 " (cutoff:3.500A)
      removed outlier: 8.458A  pdb=" N   GLU A 917 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 828 through 830
      removed outlier: 3.655A  pdb=" N   LEU A 804 " --> pdb=" O   CYS A 880 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   GLN A 801 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 923 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 27
    Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 68
      removed outlier: 6.060A  pdb=" N   LEU B  99 " --> pdb=" O   ILE B 437 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE B 423 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111
      removed outlier: 3.654A  pdb=" N   GLN B 109 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111
      removed outlier: 3.654A  pdb=" N   GLN B 109 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 199 through 201
      removed outlier: 7.062A  pdb=" N   ILE B 123 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   GLY B 163 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 125 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   GLY B 165 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   TYR B 127 " --> pdb=" O   GLY B 165 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   PHE B 167 " --> pdb=" O   TYR B 127 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   MET B 129 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ASP B 124 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL B 255 " --> pdb=" O   ASP B 124 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   TYR B 126 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   SER B 257 " --> pdb=" O   TYR B 126 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LEU B 128 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR B 258 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B 317 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 363
    Processing sheet with id=AC7, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AC8, first strand: chain 'B' and resid 509 through 512
      removed outlier: 3.514A  pdb=" N   VAL B 517 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 512 " --> pdb=" O   GLN B 515 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555
    Processing sheet with id=AD1, first strand: chain 'B' and resid 592 through 594
      removed outlier: 3.898A  pdb=" N   GLU B 594 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 671 through 674
      removed outlier: 3.590A  pdb=" N   PHE B 683 " --> pdb=" O   CYS B 671 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU B 673 " --> pdb=" O   PHE B 681 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2648
        1.33 -     1.45: 3073
        1.45 -     1.58: 7218
        1.58 -     1.70: 0
        1.70 -     1.82: 112
  Bond restraints: 13051
  Sorted by residual:
  bond pdb=" N   CYS B 415 "
       pdb=" CA  CYS B 415 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 9.10e-03 1.21e+04 1.51e+01
  bond pdb=" N   GLU A 126 "
       pdb=" CA  GLU A 126 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 9.20e-03 1.18e+04 1.44e+01
  bond pdb=" N   LYS B  87 "
       pdb=" CA  LYS B  87 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 8.70e-03 1.32e+04 1.40e+01
  bond pdb=" N   VAL B 476 "
       pdb=" CA  VAL B 476 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.17e-02 7.31e+03 1.30e+01
  bond pdb=" N   VAL A 756 "
       pdb=" CA  VAL A 756 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.11e-02 8.12e+03 1.29e+01
  ... (remaining 13046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 13231
        1.74 -     3.47: 4029
        3.47 -     5.21: 376
        5.21 -     6.94: 33
        6.94 -     8.68: 9
  Bond angle restraints: 17678
  Sorted by residual:
  angle pdb=" CA  GLY B 607 "
        pdb=" C   GLY B 607 "
        pdb=" O   GLY B 607 "
      ideal   model   delta    sigma   weight residual
     122.37  118.05    4.32 7.30e-01 1.88e+00 3.51e+01
  angle pdb=" C   ARG A 350 "
        pdb=" N   PHE A 351 "
        pdb=" CA  PHE A 351 "
      ideal   model   delta    sigma   weight residual
     120.75  129.43   -8.68 1.51e+00 4.39e-01 3.30e+01
  angle pdb=" CA  GLY B 530 "
        pdb=" C   GLY B 530 "
        pdb=" O   GLY B 530 "
      ideal   model   delta    sigma   weight residual
     122.23  118.56    3.67 6.90e-01 2.10e+00 2.83e+01
  angle pdb=" C   LEU A  79 "
        pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
      ideal   model   delta    sigma   weight residual
     122.30  115.21    7.09 1.35e+00 5.49e-01 2.76e+01
  angle pdb=" CA  GLY B  81 "
        pdb=" C   GLY B  81 "
        pdb=" O   GLY B  81 "
      ideal   model   delta    sigma   weight residual
     122.23  118.66    3.57 6.90e-01 2.10e+00 2.68e+01
  ... (remaining 17673 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.86: 8079
       22.86 -    45.72: 266
       45.72 -    68.58: 39
       68.58 -    91.44: 45
       91.44 -   114.31: 28
  Dihedral angle restraints: 8457
    sinusoidal: 3913
      harmonic: 4544
  Sorted by residual:
  dihedral pdb=" CB  CYS B 457 "
           pdb=" SG  CYS B 457 "
           pdb=" SG  CYS B 469 "
           pdb=" CB  CYS B 469 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.97   89.97     1      1.00e+01 1.00e-02 9.59e+01
  dihedral pdb=" CB  CYS A 472 "
           pdb=" SG  CYS A 472 "
           pdb=" SG  CYS A 481 "
           pdb=" CB  CYS A 481 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.83   84.83     1      1.00e+01 1.00e-02 8.74e+01
  dihedral pdb=" CB  CYS B  15 "
           pdb=" SG  CYS B  15 "
           pdb=" SG  CYS B 444 "
           pdb=" CB  CYS B 444 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.52   79.52     1      1.00e+01 1.00e-02 7.85e+01
  ... (remaining 8454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.169: 1817
       0.169 -    0.337: 213
       0.337 -    0.506: 6
       0.506 -    0.674: 0
       0.674 -    0.843: 1
  Chirality restraints: 2037
  Sorted by residual:
  chirality pdb=" C1  MAN D   4 "
            pdb=" O3  BMA D   3 "
            pdb=" C2  MAN D   4 "
            pdb=" O5  MAN D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.56    0.84 2.00e-02 2.50e+03 1.78e+03
  chirality pdb=" C1  NAG P   2 "
            pdb=" O4  NAG P   1 "
            pdb=" C2  NAG P   2 "
            pdb=" O5  NAG P   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-02 2.50e+03 2.48e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-02 2.50e+03 1.66e+02
  ... (remaining 2034 not shown)

  Planarity restraints: 2310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG O   1 "   -0.360 2.00e-02 2.50e+03   3.10e-01 1.20e+03
        pdb=" C7  NAG O   1 "    0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG O   1 "   -0.123 2.00e-02 2.50e+03
        pdb=" N2  NAG O   1 "    0.551 2.00e-02 2.50e+03
        pdb=" O7  NAG O   1 "   -0.154 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   1 "    0.351 2.00e-02 2.50e+03   3.04e-01 1.15e+03
        pdb=" C7  NAG G   1 "   -0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG G   1 "    0.099 2.00e-02 2.50e+03
        pdb=" N2  NAG G   1 "   -0.540 2.00e-02 2.50e+03
        pdb=" O7  NAG G   1 "    0.172 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "   -0.352 2.00e-02 2.50e+03   3.04e-01 1.15e+03
        pdb=" C7  NAG E   1 "    0.085 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "   -0.123 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "    0.540 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "   -0.150 2.00e-02 2.50e+03
  ... (remaining 2307 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 101
        2.44 -     3.06: 9052
        3.06 -     3.67: 18096
        3.67 -     4.29: 26307
        4.29 -     4.90: 43308
  Nonbonded interactions: 96864
  Sorted by model distance:
  nonbonded pdb=" O   SER B 134 "
            pdb="CA    CA B1002 "
     model   vdw
     1.831 2.510
  nonbonded pdb=" OD1 ASP A 243 "
            pdb="CA    CA A1101 "
     model   vdw
     1.885 2.510
  nonbonded pdb=" OG  SER A 241 "
            pdb="CA    CA A1101 "
     model   vdw
     1.904 2.510
  nonbonded pdb=" OD1 ASN A 428 "
            pdb="CA    CA A1104 "
     model   vdw
     1.914 2.510
  nonbonded pdb=" OD2 ASP B 226 "
            pdb="CA    CA B1003 "
     model   vdw
     2.011 2.510
  ... (remaining 96859 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 max=1.00 mean=0.99
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:                  0.010
  Normalize map: mean=0, sd=1:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.420
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4646
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      :  0.014   0.272  13128  Z= 1.021
  Angle     :  1.544  27.188  17872  Z= 1.120
  Chirality :  0.108   0.843   2037
  Planarity :  0.029   0.310   2295
  Dihedral  : 14.128 114.306   5446
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 64.77
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.98 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.30 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.20), residues: 1583
  helix:  1.10 (0.49), residues: 132
  sheet: -0.17 (0.24), residues: 460
  loop : -1.21 (0.18), residues: 991

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.010   0.001   TYR A 366 
 PHE   0.013   0.001   PHE A 876 
 TRP   0.014   0.001   TRP A 121 
 HIS   0.003   0.000   HIS A 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.01342 (13051)
  covalent geometry    : angle       1.50906 (17678)
  SS BOND              : bond        0.05867 (   37)
  SS BOND              : angle       1.69186 (   74)
  hydrogen bonds       : bond        0.29112 (  322)
  hydrogen bonds       : angle      10.47499 (  879)
  link_ALPHA1-3        : bond        0.01246 (    2)
  link_ALPHA1-3        : angle       5.02278 (    6)
  link_ALPHA1-6        : bond        0.00142 (    1)
  link_ALPHA1-6        : angle       0.89524 (    3)
  link_BETA1-2         : bond        0.00239 (    1)
  link_BETA1-2         : angle       2.15962 (    3)
  link_BETA1-4         : bond        0.00324 (   21)
  link_BETA1-4         : angle       1.92899 (   63)
  link_NAG-ASN         : bond        0.02075 (   15)
  link_NAG-ASN         : angle       6.21488 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.6769 (m-30) cc_final: 0.6080 (p0)
REVERT: B  335 SER cc_start: 0.6006 (p) cc_final: 0.4956 (p)
REVERT: B  518 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6917 (m)
REVERT: B  659 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5748 (mp)
  outliers start: 14
  outliers final: 5
  residues processed: 193
  average time/residue: 0.1267
  time to fit residues: 33.5279
Evaluate side-chains
  99 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 161 GLN
A 165 GLN
A 564 HIS
A 587 HIS
A 787 HIS
A 801 GLN
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 815 GLN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
B  74 ASN
B  77 ASN
B  93 GLN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 GLN
** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 539 ASN
B 623 HIS
B 628 GLN
B 670 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.088181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.067975 restraints weight = 147779.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.068494 restraints weight = 134910.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.068843 restraints weight = 124842.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.069283 restraints weight = 117299.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.069283 restraints weight = 112380.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3805 r_free = 0.3805    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      180 |
|-----------------------------------------------------------------------------|
r_final: 0.3805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6813
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13128  Z= 0.207
  Angle     :  0.970  16.390  17872  Z= 0.448
  Chirality :  0.058   0.691   2037
  Planarity :  0.005   0.078   2295
  Dihedral  : 12.805  77.139   2532
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 19.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.20), residues: 1583
  helix:  0.59 (0.39), residues: 149
  sheet:  0.07 (0.23), residues: 481
  loop : -0.86 (0.19), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 742 
 TYR   0.018   0.002   TYR B 175 
 PHE   0.035   0.003   PHE B 160 
 TRP   0.016   0.002   TRP A 947 
 HIS   0.015   0.001   HIS A 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (13051)
  covalent geometry    : angle       0.91787 (17678)
  SS BOND              : bond        0.00548 (   37)
  SS BOND              : angle       1.39619 (   74)
  hydrogen bonds       : bond        0.05875 (  322)
  hydrogen bonds       : angle       7.52194 (  879)
  link_ALPHA1-3        : bond        0.00674 (    2)
  link_ALPHA1-3        : angle       2.09071 (    6)
  link_ALPHA1-6        : bond        0.00010 (    1)
  link_ALPHA1-6        : angle       1.70796 (    3)
  link_BETA1-2         : bond        0.00365 (    1)
  link_BETA1-2         : angle       3.94800 (    3)
  link_BETA1-4         : bond        0.00801 (   21)
  link_BETA1-4         : angle       2.71872 (   63)
  link_NAG-ASN         : bond        0.00598 (   15)
  link_NAG-ASN         : angle       5.22651 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8745 (pp) cc_final: 0.8079 (pp)
REVERT: A  303 LEU cc_start: 0.9685 (mp) cc_final: 0.9378 (tp)
REVERT: A  414 PHE cc_start: 0.8846 (m-10) cc_final: 0.8531 (m-80)
REVERT: A  415 PHE cc_start: 0.8648 (t80) cc_final: 0.8203 (t80)
REVERT: A  433 LEU cc_start: 0.7688 (tp) cc_final: 0.7451 (tp)
REVERT: A  619 PHE cc_start: 0.8390 (t80) cc_final: 0.7972 (t80)
REVERT: B  131 LEU cc_start: 0.8116 (mp) cc_final: 0.7775 (tp)
REVERT: B  164 PHE cc_start: 0.9241 (t80) cc_final: 0.8246 (t80)
REVERT: B  236 MET cc_start: 0.9375 (mmp) cc_final: 0.8877 (mmm)
REVERT: B  256 PHE cc_start: 0.9083 (t80) cc_final: 0.8523 (t80)
REVERT: B  315 PHE cc_start: 0.9137 (m-80) cc_final: 0.8912 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1367
  time to fit residues: 22.2070
Evaluate side-chains
  82 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 129 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 98 optimal weight:    0.1980
   chunk 104 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 117 optimal weight:    9.9990
   chunk 149 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   overall best weight:    5.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 624 HIS
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN
** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.076239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.058167 restraints weight = 156853.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.058524 restraints weight = 141279.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.059092 restraints weight = 129331.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.059367 restraints weight = 121762.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.059747 restraints weight = 116618.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      180 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3747 r_free = 0.3747    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      265 |
|-----------------------------------------------------------------------------|
r_final: 0.3747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.4876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090  13128  Z= 0.243
  Angle     :  0.892  15.271  17872  Z= 0.431
  Chirality :  0.053   0.492   2037
  Planarity :  0.005   0.058   2295
  Dihedral  :  9.631  56.628   2532
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 23.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.20), residues: 1583
  helix:  0.24 (0.40), residues: 152
  sheet: -0.09 (0.22), residues: 497
  loop : -0.92 (0.19), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 323 
 TYR   0.025   0.003   TYR A 920 
 PHE   0.024   0.003   PHE A 722 
 TRP   0.017   0.002   TRP A 100 
 HIS   0.010   0.002   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (13051)
  covalent geometry    : angle       0.84613 (17678)
  SS BOND              : bond        0.00478 (   37)
  SS BOND              : angle       1.34969 (   74)
  hydrogen bonds       : bond        0.05055 (  322)
  hydrogen bonds       : angle       7.01846 (  879)
  link_ALPHA1-3        : bond        0.01070 (    2)
  link_ALPHA1-3        : angle       1.44898 (    6)
  link_ALPHA1-6        : bond        0.00376 (    1)
  link_ALPHA1-6        : angle       1.77671 (    3)
  link_BETA1-2         : bond        0.00339 (    1)
  link_BETA1-2         : angle       3.04834 (    3)
  link_BETA1-4         : bond        0.00632 (   21)
  link_BETA1-4         : angle       2.62346 (   63)
  link_NAG-ASN         : bond        0.00543 (   15)
  link_NAG-ASN         : angle       4.59472 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8846 (pp) cc_final: 0.7927 (pp)
REVERT: A  228 ASP cc_start: 0.8751 (m-30) cc_final: 0.8546 (m-30)
REVERT: A  303 LEU cc_start: 0.9634 (mp) cc_final: 0.9421 (tp)
REVERT: A  414 PHE cc_start: 0.9163 (m-10) cc_final: 0.8849 (m-80)
REVERT: A  415 PHE cc_start: 0.8937 (t80) cc_final: 0.8370 (t80)
REVERT: A  446 TYR cc_start: 0.8867 (m-10) cc_final: 0.8411 (m-10)
REVERT: A  458 LEU cc_start: 0.8270 (tp) cc_final: 0.7902 (tp)
REVERT: A  567 LEU cc_start: 0.9322 (tp) cc_final: 0.8998 (mm)
REVERT: A  897 PHE cc_start: 0.6886 (p90) cc_final: 0.6305 (p90)
REVERT: B  131 LEU cc_start: 0.8315 (mp) cc_final: 0.7758 (tp)
REVERT: B  212 PHE cc_start: 0.9322 (t80) cc_final: 0.8874 (t80)
REVERT: B  236 MET cc_start: 0.9388 (mmp) cc_final: 0.8878 (mmm)
REVERT: B  256 PHE cc_start: 0.9220 (t80) cc_final: 0.8638 (t80)
REVERT: B  315 PHE cc_start: 0.9300 (m-80) cc_final: 0.9000 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1373
  time to fit residues: 16.2833
Evaluate side-chains
  65 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 154 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 136 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 816 GLN
** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN
** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.077062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.059819 restraints weight = 154170.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.060242 restraints weight = 137597.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.060635 restraints weight = 125724.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.060883 restraints weight = 117593.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.061109 restraints weight = 111575.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      265 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      250 |
|-----------------------------------------------------------------------------|
r_final: 0.3658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.5208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13128  Z= 0.140
  Angle     :  0.769  14.135  17872  Z= 0.354
  Chirality :  0.050   0.523   2037
  Planarity :  0.004   0.055   2295
  Dihedral  :  8.429  59.444   2532
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.64 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.20), residues: 1583
  helix:  0.69 (0.41), residues: 152
  sheet:  0.04 (0.22), residues: 506
  loop : -0.76 (0.20), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 323 
 TYR   0.020   0.002   TYR A 920 
 PHE   0.016   0.002   PHE A 876 
 TRP   0.015   0.001   TRP A 703 
 HIS   0.006   0.001   HIS A 787 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13051)
  covalent geometry    : angle       0.71443 (17678)
  SS BOND              : bond        0.00276 (   37)
  SS BOND              : angle       1.10653 (   74)
  hydrogen bonds       : bond        0.03841 (  322)
  hydrogen bonds       : angle       6.45027 (  879)
  link_ALPHA1-3        : bond        0.01310 (    2)
  link_ALPHA1-3        : angle       1.70891 (    6)
  link_ALPHA1-6        : bond        0.00019 (    1)
  link_ALPHA1-6        : angle       1.57427 (    3)
  link_BETA1-2         : bond        0.00258 (    1)
  link_BETA1-2         : angle       3.19612 (    3)
  link_BETA1-4         : bond        0.00659 (   21)
  link_BETA1-4         : angle       2.46682 (   63)
  link_NAG-ASN         : bond        0.00461 (   15)
  link_NAG-ASN         : angle       4.77776 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8742 (pp) cc_final: 0.8053 (pp)
REVERT: A  414 PHE cc_start: 0.9267 (m-10) cc_final: 0.8971 (m-80)
REVERT: A  415 PHE cc_start: 0.9029 (t80) cc_final: 0.8497 (t80)
REVERT: A  433 LEU cc_start: 0.7505 (tp) cc_final: 0.7238 (tp)
REVERT: A  446 TYR cc_start: 0.8791 (m-10) cc_final: 0.8283 (m-10)
REVERT: A  458 LEU cc_start: 0.8047 (tp) cc_final: 0.7786 (tp)
REVERT: A  505 LEU cc_start: 0.9729 (tp) cc_final: 0.9520 (pp)
REVERT: A  529 LEU cc_start: 0.9083 (tp) cc_final: 0.8508 (tt)
REVERT: B   38 MET cc_start: 0.9290 (mmp) cc_final: 0.9050 (mmm)
REVERT: B  128 LEU cc_start: 0.9668 (mt) cc_final: 0.9467 (mt)
REVERT: B  131 LEU cc_start: 0.8406 (mp) cc_final: 0.7982 (tp)
REVERT: B  135 MET cc_start: 0.8429 (mpp) cc_final: 0.8071 (mpp)
REVERT: B  212 PHE cc_start: 0.9336 (t80) cc_final: 0.8843 (t80)
REVERT: B  236 MET cc_start: 0.9396 (mmp) cc_final: 0.8863 (mmm)
REVERT: B  256 PHE cc_start: 0.9288 (t80) cc_final: 0.8657 (t80)
REVERT: B  315 PHE cc_start: 0.9306 (m-80) cc_final: 0.9065 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1357
  time to fit residues: 16.6629
Evaluate side-chains
  62 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 45 optimal weight:   30.0000
   chunk 157 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 133 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 117 optimal weight:    9.9990
   chunk 29 optimal weight:   20.0000
   chunk 31 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0170
   overall best weight:    2.4622

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

Flipped N/Q/H residues before XYZ refinement:
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.075375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.058181 restraints weight = 155548.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.058505 restraints weight = 138121.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.058949 restraints weight = 127552.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.059157 restraints weight = 119206.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.059399 restraints weight = 113549.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      250 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.5706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13128  Z= 0.140
  Angle     :  0.730  12.669  17872  Z= 0.342
  Chirality :  0.048   0.458   2037
  Planarity :  0.004   0.053   2295
  Dihedral  :  8.035  58.568   2532
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.20 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.21), residues: 1583
  helix:  0.74 (0.42), residues: 152
  sheet:  0.25 (0.23), residues: 499
  loop : -0.75 (0.20), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 426 
 TYR   0.016   0.002   TYR B 528 
 PHE   0.013   0.002   PHE A 876 
 TRP   0.012   0.001   TRP A 100 
 HIS   0.012   0.001   HIS A 896 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (13051)
  covalent geometry    : angle       0.68502 (17678)
  SS BOND              : bond        0.00199 (   37)
  SS BOND              : angle       0.95296 (   74)
  hydrogen bonds       : bond        0.03638 (  322)
  hydrogen bonds       : angle       6.25505 (  879)
  link_ALPHA1-3        : bond        0.01259 (    2)
  link_ALPHA1-3        : angle       1.63639 (    6)
  link_ALPHA1-6        : bond        0.00105 (    1)
  link_ALPHA1-6        : angle       1.67981 (    3)
  link_BETA1-2         : bond        0.00110 (    1)
  link_BETA1-2         : angle       3.01536 (    3)
  link_BETA1-4         : bond        0.00616 (   21)
  link_BETA1-4         : angle       2.34351 (   63)
  link_NAG-ASN         : bond        0.00335 (   15)
  link_NAG-ASN         : angle       4.14459 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8773 (pp) cc_final: 0.8131 (pp)
REVERT: A  165 GLN cc_start: 0.9542 (tp40) cc_final: 0.9314 (tp40)
REVERT: A  228 ASP cc_start: 0.8986 (m-30) cc_final: 0.8544 (m-30)
REVERT: A  414 PHE cc_start: 0.9240 (m-10) cc_final: 0.8942 (m-80)
REVERT: A  415 PHE cc_start: 0.9114 (t80) cc_final: 0.8676 (t80)
REVERT: A  446 TYR cc_start: 0.8815 (m-10) cc_final: 0.8268 (m-10)
REVERT: B   38 MET cc_start: 0.9251 (mmp) cc_final: 0.9001 (mmm)
REVERT: B  131 LEU cc_start: 0.8427 (mp) cc_final: 0.8139 (tp)
REVERT: B  135 MET cc_start: 0.8588 (mpp) cc_final: 0.8361 (mpp)
REVERT: B  212 PHE cc_start: 0.9321 (t80) cc_final: 0.8790 (t80)
REVERT: B  236 MET cc_start: 0.9371 (mmp) cc_final: 0.8718 (mmm)
REVERT: B  256 PHE cc_start: 0.9280 (t80) cc_final: 0.8777 (t80)
REVERT: B  315 PHE cc_start: 0.9282 (m-80) cc_final: 0.9024 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1366
  time to fit residues: 14.8142
Evaluate side-chains
  61 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 146 optimal weight:    0.7980
   chunk 135 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 52 optimal weight:    0.2980
   chunk 46 optimal weight:    6.9990
   chunk 92 optimal weight:   40.0000
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.073687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.056767 restraints weight = 157114.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.057184 restraints weight = 140512.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.057583 restraints weight = 128461.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.057798 restraints weight = 118261.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.058044 restraints weight = 112254.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      264 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.6219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13128  Z= 0.144
  Angle     :  0.724  12.354  17872  Z= 0.340
  Chirality :  0.048   0.434   2037
  Planarity :  0.004   0.052   2295
  Dihedral  :  8.092  64.860   2532
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.84 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.21), residues: 1583
  helix:  0.39 (0.40), residues: 160
  sheet:  0.19 (0.22), residues: 505
  loop : -0.77 (0.20), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 106 
 TYR   0.029   0.001   TYR A 327 
 PHE   0.016   0.002   PHE B 164 
 TRP   0.024   0.002   TRP A 157 
 HIS   0.005   0.001   HIS A 896 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13051)
  covalent geometry    : angle       0.68268 (17678)
  SS BOND              : bond        0.00556 (   37)
  SS BOND              : angle       0.96610 (   74)
  hydrogen bonds       : bond        0.03590 (  322)
  hydrogen bonds       : angle       6.27202 (  879)
  link_ALPHA1-3        : bond        0.01073 (    2)
  link_ALPHA1-3        : angle       1.62708 (    6)
  link_ALPHA1-6        : bond        0.00007 (    1)
  link_ALPHA1-6        : angle       1.71079 (    3)
  link_BETA1-2         : bond        0.00094 (    1)
  link_BETA1-2         : angle       2.99888 (    3)
  link_BETA1-4         : bond        0.00626 (   21)
  link_BETA1-4         : angle       2.26502 (   63)
  link_NAG-ASN         : bond        0.00325 (   15)
  link_NAG-ASN         : angle       3.88663 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8681 (pp) cc_final: 0.8035 (pp)
REVERT: A  228 ASP cc_start: 0.9011 (m-30) cc_final: 0.8566 (m-30)
REVERT: A  310 MET cc_start: 0.9486 (mmp) cc_final: 0.8998 (tpp)
REVERT: A  414 PHE cc_start: 0.9264 (m-10) cc_final: 0.8994 (m-80)
REVERT: A  415 PHE cc_start: 0.9200 (t80) cc_final: 0.8875 (t80)
REVERT: A  446 TYR cc_start: 0.8827 (m-10) cc_final: 0.8289 (m-10)
REVERT: A  529 LEU cc_start: 0.9237 (tt) cc_final: 0.8910 (mm)
REVERT: B   38 MET cc_start: 0.9289 (mmp) cc_final: 0.9037 (mmm)
REVERT: B  130 ASP cc_start: 0.8089 (t0) cc_final: 0.7715 (t0)
REVERT: B  131 LEU cc_start: 0.8341 (mp) cc_final: 0.7925 (tp)
REVERT: B  212 PHE cc_start: 0.9363 (t80) cc_final: 0.8824 (t80)
REVERT: B  236 MET cc_start: 0.9364 (mmp) cc_final: 0.8753 (mmm)
REVERT: B  256 PHE cc_start: 0.9253 (t80) cc_final: 0.8775 (t80)
REVERT: B  315 PHE cc_start: 0.9298 (m-80) cc_final: 0.9052 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1276
  time to fit residues: 13.8140
Evaluate side-chains
  59 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 154 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 93 optimal weight:   20.0000
   chunk 149 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 GLN
A 191 GLN
** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 GLN
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 787 HIS
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 GLN
B  92 HIS
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 551 ASN
B 628 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.065795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.049400 restraints weight = 165966.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.049556 restraints weight = 150900.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.049793 restraints weight = 139731.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.050043 restraints weight = 131764.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.050147 restraints weight = 126563.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      264 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      262 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.7809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083  13128  Z= 0.291
  Angle     :  0.971  13.377  17872  Z= 0.481
  Chirality :  0.053   0.425   2037
  Planarity :  0.006   0.061   2295
  Dihedral  :  8.748  61.193   2532
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 35.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.98 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.20), residues: 1583
  helix: -0.88 (0.37), residues: 157
  sheet: -0.15 (0.23), residues: 491
  loop : -1.08 (0.20), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 317 
 TYR   0.026   0.003   TYR B 127 
 PHE   0.027   0.003   PHE A 240 
 TRP   0.026   0.003   TRP A 703 
 HIS   0.012   0.002   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (13051)
  covalent geometry    : angle       0.92962 (17678)
  SS BOND              : bond        0.00518 (   37)
  SS BOND              : angle       1.75186 (   74)
  hydrogen bonds       : bond        0.05084 (  322)
  hydrogen bonds       : angle       7.81542 (  879)
  link_ALPHA1-3        : bond        0.00658 (    2)
  link_ALPHA1-3        : angle       1.96259 (    6)
  link_ALPHA1-6        : bond        0.00428 (    1)
  link_ALPHA1-6        : angle       2.82600 (    3)
  link_BETA1-2         : bond        0.00611 (    1)
  link_BETA1-2         : angle       3.52955 (    3)
  link_BETA1-4         : bond        0.00549 (   21)
  link_BETA1-4         : angle       2.43508 (   63)
  link_NAG-ASN         : bond        0.00680 (   15)
  link_NAG-ASN         : angle       4.45396 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8841 (pp) cc_final: 0.7906 (pp)
REVERT: A  415 PHE cc_start: 0.9579 (t80) cc_final: 0.9353 (t80)
REVERT: A  446 TYR cc_start: 0.9188 (m-10) cc_final: 0.8564 (m-80)
REVERT: A  925 MET cc_start: 0.1956 (pmm) cc_final: 0.1703 (pmm)
REVERT: B  127 TYR cc_start: 0.9263 (t80) cc_final: 0.8801 (t80)
REVERT: B  128 LEU cc_start: 0.9813 (mt) cc_final: 0.9587 (mt)
REVERT: B  130 ASP cc_start: 0.9145 (t0) cc_final: 0.8941 (t0)
REVERT: B  131 LEU cc_start: 0.9083 (mp) cc_final: 0.8844 (tp)
REVERT: B  236 MET cc_start: 0.9674 (mmp) cc_final: 0.9141 (mmm)
REVERT: B  256 PHE cc_start: 0.9653 (t80) cc_final: 0.9166 (t80)
REVERT: B  315 PHE cc_start: 0.9594 (m-80) cc_final: 0.9283 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1354
  time to fit residues: 13.7773
Evaluate side-chains
  54 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 152 optimal weight:   30.0000
   chunk 128 optimal weight:    0.3980
   chunk 18 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 149 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 147 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.063164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.043373 restraints weight = 134122.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.043135 restraints weight = 129076.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.043456 restraints weight = 121856.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.043456 restraints weight = 115742.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.043456 restraints weight = 115742.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      262 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      263 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.7905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13128  Z= 0.154
  Angle     :  0.765  13.070  17872  Z= 0.364
  Chirality :  0.048   0.431   2037
  Planarity :  0.004   0.053   2295
  Dihedral  :  8.485  65.299   2532
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.21), residues: 1583
  helix: -0.33 (0.39), residues: 159
  sheet: -0.15 (0.23), residues: 502
  loop : -0.99 (0.20), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 521 
 TYR   0.023   0.002   TYR B 528 
 PHE   0.014   0.002   PHE A 637 
 TRP   0.022   0.002   TRP A 703 
 HIS   0.005   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (13051)
  covalent geometry    : angle       0.71804 (17678)
  SS BOND              : bond        0.00278 (   37)
  SS BOND              : angle       1.22184 (   74)
  hydrogen bonds       : bond        0.03844 (  322)
  hydrogen bonds       : angle       7.13021 (  879)
  link_ALPHA1-3        : bond        0.00923 (    2)
  link_ALPHA1-3        : angle       1.68607 (    6)
  link_ALPHA1-6        : bond        0.00235 (    1)
  link_ALPHA1-6        : angle       1.80318 (    3)
  link_BETA1-2         : bond        0.00033 (    1)
  link_BETA1-2         : angle       3.15855 (    3)
  link_BETA1-4         : bond        0.00602 (   21)
  link_BETA1-4         : angle       2.30737 (   63)
  link_NAG-ASN         : bond        0.00428 (   15)
  link_NAG-ASN         : angle       4.30624 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8530 (pp) cc_final: 0.7743 (pp)
REVERT: A  228 ASP cc_start: 0.9418 (m-30) cc_final: 0.9199 (m-30)
REVERT: A  446 TYR cc_start: 0.9212 (m-10) cc_final: 0.8687 (m-10)
REVERT: A  652 LEU cc_start: 0.9191 (mm) cc_final: 0.8464 (pp)
REVERT: B  127 TYR cc_start: 0.9261 (t80) cc_final: 0.8844 (t80)
REVERT: B  236 MET cc_start: 0.9522 (mmp) cc_final: 0.9287 (mmm)
REVERT: B  256 PHE cc_start: 0.9615 (t80) cc_final: 0.9113 (t80)
REVERT: B  315 PHE cc_start: 0.9564 (m-80) cc_final: 0.9275 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1013
  time to fit residues: 10.3351
Evaluate side-chains
  48 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 102 optimal weight:   20.0000
   chunk 147 optimal weight:   40.0000
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 128 optimal weight:    8.9990
   chunk 93 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 624 HIS
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 GLN
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.062799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.042136 restraints weight = 136848.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.042260 restraints weight = 128501.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.042260 restraints weight = 124511.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.042260 restraints weight = 124511.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.042260 restraints weight = 124511.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      263 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      264 |
|-----------------------------------------------------------------------------|
r_final: 0.3307
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.8129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13128  Z= 0.149
  Angle     :  0.748  12.524  17872  Z= 0.355
  Chirality :  0.048   0.421   2037
  Planarity :  0.005   0.098   2295
  Dihedral  :  8.481  72.041   2532
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 21.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.20), residues: 1583
  helix: -0.25 (0.39), residues: 159
  sheet: -0.14 (0.22), residues: 501
  loop : -1.01 (0.20), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 317 
 TYR   0.015   0.002   TYR A 163 
 PHE   0.013   0.002   PHE A 637 
 TRP   0.018   0.002   TRP A 703 
 HIS   0.005   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (13051)
  covalent geometry    : angle       0.70615 (17678)
  SS BOND              : bond        0.00265 (   37)
  SS BOND              : angle       1.13600 (   74)
  hydrogen bonds       : bond        0.03774 (  322)
  hydrogen bonds       : angle       6.97612 (  879)
  link_ALPHA1-3        : bond        0.00862 (    2)
  link_ALPHA1-3        : angle       1.65619 (    6)
  link_ALPHA1-6        : bond        0.00169 (    1)
  link_ALPHA1-6        : angle       1.92871 (    3)
  link_BETA1-2         : bond        0.00054 (    1)
  link_BETA1-2         : angle       3.15464 (    3)
  link_BETA1-4         : bond        0.00639 (   21)
  link_BETA1-4         : angle       2.30477 (   63)
  link_NAG-ASN         : bond        0.00373 (   15)
  link_NAG-ASN         : angle       3.94567 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8470 (pp) cc_final: 0.7802 (pp)
REVERT: A  228 ASP cc_start: 0.9383 (m-30) cc_final: 0.9101 (m-30)
REVERT: A  415 PHE cc_start: 0.9679 (t80) cc_final: 0.9428 (t80)
REVERT: A  446 TYR cc_start: 0.9136 (m-10) cc_final: 0.8645 (m-10)
REVERT: A  652 LEU cc_start: 0.9246 (mm) cc_final: 0.8462 (pp)
REVERT: B  127 TYR cc_start: 0.9289 (t80) cc_final: 0.8894 (t80)
REVERT: B  236 MET cc_start: 0.9548 (mmp) cc_final: 0.9302 (mmm)
REVERT: B  256 PHE cc_start: 0.9629 (t80) cc_final: 0.9180 (t80)
REVERT: B  315 PHE cc_start: 0.9570 (m-80) cc_final: 0.9271 (m-80)
REVERT: B  334 LYS cc_start: 0.6805 (mmmt) cc_final: 0.5150 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1201
  time to fit residues: 10.4583
Evaluate side-chains
  50 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 148 optimal weight:   20.0000
   chunk 117 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 136 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.062139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.041648 restraints weight = 136525.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 16)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.041899 restraints weight = 128380.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.042163 restraints weight = 122094.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.042391 restraints weight = 117284.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.042391 restraints weight = 111731.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      264 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      265 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.8431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13128  Z= 0.152
  Angle     :  0.752  12.114  17872  Z= 0.356
  Chirality :  0.050   0.646   2037
  Planarity :  0.004   0.057   2295
  Dihedral  :  8.562  78.301   2532
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.20), residues: 1583
  helix: -0.75 (0.37), residues: 175
  sheet: -0.17 (0.23), residues: 484
  loop : -1.03 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 312 
 TYR   0.016   0.002   TYR A 163 
 PHE   0.014   0.002   PHE A  19 
 TRP   0.020   0.002   TRP A 703 
 HIS   0.005   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (13051)
  covalent geometry    : angle       0.70877 (17678)
  SS BOND              : bond        0.00257 (   37)
  SS BOND              : angle       1.11021 (   74)
  hydrogen bonds       : bond        0.03684 (  322)
  hydrogen bonds       : angle       6.95682 (  879)
  link_ALPHA1-3        : bond        0.00733 (    2)
  link_ALPHA1-3        : angle       1.63224 (    6)
  link_ALPHA1-6        : bond        0.00218 (    1)
  link_ALPHA1-6        : angle       1.91175 (    3)
  link_BETA1-2         : bond        0.00105 (    1)
  link_BETA1-2         : angle       3.20235 (    3)
  link_BETA1-4         : bond        0.00597 (   21)
  link_BETA1-4         : angle       2.34860 (   63)
  link_NAG-ASN         : bond        0.00413 (   15)
  link_NAG-ASN         : angle       4.01547 (   45)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8499 (pp) cc_final: 0.7784 (pp)
REVERT: A  415 PHE cc_start: 0.9677 (t80) cc_final: 0.9398 (t80)
REVERT: A  446 TYR cc_start: 0.9059 (m-10) cc_final: 0.8543 (m-10)
REVERT: A  652 LEU cc_start: 0.9235 (mm) cc_final: 0.8409 (pp)
REVERT: A  654 VAL cc_start: 0.8362 (t) cc_final: 0.8061 (m)
REVERT: B  127 TYR cc_start: 0.9316 (t80) cc_final: 0.9043 (t80)
REVERT: B  129 MET cc_start: 0.9075 (ttp) cc_final: 0.8678 (tpt)
REVERT: B  236 MET cc_start: 0.9528 (mmp) cc_final: 0.9267 (mmm)
REVERT: B  256 PHE cc_start: 0.9645 (t80) cc_final: 0.9189 (t80)
REVERT: B  315 PHE cc_start: 0.9604 (m-80) cc_final: 0.9276 (m-80)
REVERT: B  334 LYS cc_start: 0.6756 (mmmt) cc_final: 0.5113 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1177
  time to fit residues: 10.1692
Evaluate side-chains
  52 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 144 optimal weight:   50.0000
   chunk 49 optimal weight:   20.0000
   chunk 145 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 113 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 22 optimal weight:    6.9990
   chunk 133 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
A   2 ASN
A  46 GLN
A 624 HIS
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 GLN
** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.059245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.040422 restraints weight = 139131.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.040014 restraints weight = 136569.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.040255 restraints weight = 128244.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.040495 restraints weight = 121988.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.040542 restraints weight = 117388.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      265 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
r_final: 0.3322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.9186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100  13128  Z= 0.201
  Angle     :  0.809  12.415  17872  Z= 0.393
  Chirality :  0.051   0.660   2037
  Planarity :  0.005   0.059   2295
  Dihedral  :  8.998  86.199   2532
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 27.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.44 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.20), residues: 1583
  helix: -1.01 (0.36), residues: 170
  sheet: -0.48 (0.23), residues: 494
  loop : -1.09 (0.20), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  78 
 TYR   0.019   0.002   TYR B 380 
 PHE   0.019   0.002   PHE A 240 
 TRP   0.029   0.002   TRP A 703 
 HIS   0.008   0.002   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (13051)
  covalent geometry    : angle       0.77046 (17678)
  SS BOND              : bond        0.00368 (   37)
  SS BOND              : angle       1.32210 (   74)
  hydrogen bonds       : bond        0.04065 (  322)
  hydrogen bonds       : angle       7.50223 (  879)
  link_ALPHA1-3        : bond        0.00534 (    2)
  link_ALPHA1-3        : angle       1.81076 (    6)
  link_ALPHA1-6        : bond        0.00038 (    1)
  link_ALPHA1-6        : angle       2.41364 (    3)
  link_BETA1-2         : bond        0.00385 (    1)
  link_BETA1-2         : angle       3.44861 (    3)
  link_BETA1-4         : bond        0.00582 (   21)
  link_BETA1-4         : angle       2.37789 (   63)
  link_NAG-ASN         : bond        0.00480 (   15)
  link_NAG-ASN         : angle       3.80668 (   45)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2767.98 seconds
wall clock time: 48 minutes 21.80 seconds (2901.80 seconds total)