Starting phenix.real_space_refine
on Tue Feb  3 23:23:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zwc_60523/02_2026/8zwc_60523.cif"
  }
  resolution = 3.19
  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=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4910      2.51       5
     N    1287      2.21       5
     O    1372      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 568, 4597
          Classifications: {'peptide': 568}
          Link IDs: {'PTRANS': 28, 'TRANS': 539}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3011
          Classifications: {'peptide': 381}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360}
          Chain breaks: 6
  Time building chain proxies: 1.79, per 1000 atoms: 0.24
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (83.3, 89.25, 130.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1372      8.00
     N    1287      7.00
     C    4910      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  96 " - pdb=" SG  CYS B 105 " 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
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 279.5 milliseconds
  

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1802

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      53.6% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 31
    Processing helix  chain 'A' and resid 42 through 66
      Proline residue:  A  53  - end of helix
      removed outlier: 3.595A  pdb=" N   MET A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   MET A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 78
    Processing helix  chain 'A' and resid 101 through 121
    Processing helix  chain 'A' and resid 122 through 125
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 3.601A  pdb=" N   ARG A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS A 132 " --> pdb=" O   HIS A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 163
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 176 through 191
      removed outlier: 3.573A  pdb=" N   GLU A 181 " --> pdb=" O   PRO A 177 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 199 through 202
      removed outlier: 4.240A  pdb=" N   GLY A 202 " --> pdb=" O   PRO A 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 199 through 202'
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 3.746A  pdb=" N   LEU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 412
      removed outlier: 3.513A  pdb=" N   VAL A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER A 403 " --> pdb=" O   MET A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 421
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 3.758A  pdb=" N   LYS A 434 " --> pdb=" O   GLN A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 457
      removed outlier: 3.759A  pdb=" N   THR A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 487
      removed outlier: 3.585A  pdb=" N   GLN A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 487 " --> pdb=" O   ARG A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 494
      removed outlier: 3.530A  pdb=" N   GLY A 494 " --> pdb=" O   PRO A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 514
      removed outlier: 3.517A  pdb=" N   ARG A 511 " --> pdb=" O   GLN A 507 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LYS A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 527
      removed outlier: 3.519A  pdb=" N   ARG A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 536
      removed outlier: 3.874A  pdb=" N   GLU A 536 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 594
      removed outlier: 4.064A  pdb=" N   TRP A 583 " --> pdb=" O   LYS A 579 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 657
      removed outlier: 4.133A  pdb=" N   ASN A 656 " --> pdb=" O   TYR A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 695
      removed outlier: 3.538A  pdb=" N   GLN A 682 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 35
      No H-bonds generated for 'chain 'B' and resid 33 through 35'
    Processing helix  chain 'B' and resid 46 through 69
      removed outlier: 3.523A  pdb=" N   GLN B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 121
    Processing helix  chain 'B' and resid 122 through 130
    Processing helix  chain 'B' and resid 131 through 149
      removed outlier: 4.242A  pdb=" N   LEU B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 158
    Processing helix  chain 'B' and resid 171 through 186
      removed outlier: 3.546A  pdb=" N   LYS B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 180 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 215
      removed outlier: 3.698A  pdb=" N   LYS B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 260
    Processing helix  chain 'B' and resid 566 through 574
      removed outlier: 3.660A  pdb=" N   GLU B 570 " --> pdb=" O   ALA B 566 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS B 573 " --> pdb=" O   GLU B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 588
      removed outlier: 3.586A  pdb=" N   GLY B 581 " --> pdb=" O   ALA B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 643
      removed outlier: 3.682A  pdb=" N   LEU B 635 " --> pdb=" O   GLN B 631 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER B 638 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 641 " --> pdb=" O   HIS B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 690
      No H-bonds generated for 'chain 'B' and resid 688 through 690'
    Processing helix  chain 'B' and resid 691 through 700
      removed outlier: 3.779A  pdb=" N   LYS B 695 " --> pdb=" O   SER B 691 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS B 697 " --> pdb=" O   SER B 693 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN B 698 " --> pdb=" O   GLY B 694 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU B 700 " --> pdb=" O   ALA B 696 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18
      removed outlier: 6.900A  pdb=" N   VAL A   6 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR A  16 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL A   4 " --> pdb=" O   TYR A  16 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   THR A  18 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LYS A   2 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   CYS A  89 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR A  70 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ARG B  76 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   PHE A  72 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU B  74 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS B  81 " --> pdb=" O   CYS B  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE B  19 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   PHE B  18 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE B  40 " --> pdb=" O   PHE B  18 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LEU B  20 " --> pdb=" O   CYS B  38 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS B  38 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 222
      removed outlier: 6.897A  pdb=" N   LEU A 211 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   PHE A 220 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ALA A 209 " --> pdb=" O   PHE A 220 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   SER A 222 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   LEU A 207 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA A 206 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ARG A 385 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   HIS A 208 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A 365 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A 353 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 555
      removed outlier: 7.940A  pdb=" N   LEU A 541 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   LEU A 672 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   HIS A 543 " --> pdb=" O   LEU A 670 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TRP A 614 " --> pdb=" O   TYR A 665 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 669 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE A 607 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 602 " --> pdb=" O   CYS A 609 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 599 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG B 652 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU B 648 " --> pdb=" O   GLN A 603 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   TYR B 647 " --> pdb=" O   CYS B 662 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   ALA B 657 " --> pdb=" O   GLN B 672 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLN B 672 " --> pdb=" O   ALA B 657 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 203
      removed outlier: 5.389A  pdb=" N   ILE B 200 " --> pdb=" O   TYR B 196 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   TYR B 196 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER B 202 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA B 191 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU B 556 " --> pdb=" O   ALA B 191 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B 554 " --> pdb=" O   CYS B 193 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU B 553 " --> pdb=" O   HIS B 546 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1233 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: 0.98

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2422
        1.34 -     1.46: 1179
        1.46 -     1.58: 4122
        1.58 -     1.70: 0
        1.70 -     1.81: 56
  Bond restraints: 7779
  Sorted by residual:
  bond pdb=" N   LEU A 487 "
       pdb=" CA  LEU A 487 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.48e+00
  bond pdb=" N   PHE A 486 "
       pdb=" CA  PHE A 486 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.18e-02 7.18e+03 6.74e+00
  bond pdb=" N   CYS B 183 "
       pdb=" CA  CYS B 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.64e+00
  bond pdb=" N   THR A 488 "
       pdb=" CA  THR A 488 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.33e-02 5.65e+03 5.57e+00
  bond pdb=" N   GLN B 184 "
       pdb=" CA  GLN B 184 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 5.01e+00
  ... (remaining 7774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 10420
        2.23 -     4.45: 110
        4.45 -     6.68: 7
        6.68 -     8.90: 1
        8.90 -    11.13: 1
  Bond angle restraints: 10539
  Sorted by residual:
  angle pdb=" N   PRO B 187 "
        pdb=" CA  PRO B 187 "
        pdb=" C   PRO B 187 "
      ideal   model   delta    sigma   weight residual
     112.47  123.60  -11.13 2.06e+00 2.36e-01 2.92e+01
  angle pdb=" CA  PHE A 486 "
        pdb=" C   PHE A 486 "
        pdb=" O   PHE A 486 "
      ideal   model   delta    sigma   weight residual
     119.78  116.17    3.61 1.19e+00 7.06e-01 9.19e+00
  angle pdb=" C   ASN A 485 "
        pdb=" N   PHE A 486 "
        pdb=" CA  PHE A 486 "
      ideal   model   delta    sigma   weight residual
     122.73  117.86    4.87 1.61e+00 3.86e-01 9.16e+00
  angle pdb=" O   ARG B 185 "
        pdb=" C   ARG B 185 "
        pdb=" N   SER B 186 "
      ideal   model   delta    sigma   weight residual
     122.15  125.49   -3.34 1.14e+00 7.69e-01 8.56e+00
  angle pdb=" CA  ARG B 185 "
        pdb=" C   ARG B 185 "
        pdb=" O   ARG B 185 "
      ideal   model   delta    sigma   weight residual
     120.42  117.43    2.99 1.06e+00 8.90e-01 7.97e+00
  ... (remaining 10534 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 4238
       16.08 -    32.17: 334
       32.17 -    48.25: 86
       48.25 -    64.34: 16
       64.34 -    80.42: 4
  Dihedral angle restraints: 4678
    sinusoidal: 1903
      harmonic: 2775
  Sorted by residual:
  dihedral pdb=" CB  CYS B  96 "
           pdb=" SG  CYS B  96 "
           pdb=" SG  CYS B 105 "
           pdb=" CB  CYS B 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.48   54.48     1      1.00e+01 1.00e-02 4.02e+01
  dihedral pdb=" CA  ASP A 126 "
           pdb=" CB  ASP A 126 "
           pdb=" CG  ASP A 126 "
           pdb=" OD1 ASP A 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.80   53.80     1      2.00e+01 2.50e-03 9.82e+00
  dihedral pdb=" CG  ARG A 657 "
           pdb=" CD  ARG A 657 "
           pdb=" NE  ARG A 657 "
           pdb=" CZ  ARG A 657 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.40   42.60     2      1.50e+01 4.44e-03 9.78e+00
  ... (remaining 4675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1109
       0.070 -    0.140: 80
       0.140 -    0.209: 2
       0.209 -    0.279: 1
       0.279 -    0.349: 1
  Chirality restraints: 1193
  Sorted by residual:
  chirality pdb=" CA  PRO B 187 "
            pdb=" N   PRO B 187 "
            pdb=" C   PRO B 187 "
            pdb=" CB  PRO B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  ARG B 185 "
            pdb=" N   ARG B 185 "
            pdb=" C   ARG B 185 "
            pdb=" CB  ARG B 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CB  ILE B 143 "
            pdb=" CA  ILE B 143 "
            pdb=" CG1 ILE B 143 "
            pdb=" CG2 ILE B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.54e-01
  ... (remaining 1190 not shown)

  Planarity restraints: 1329
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 239 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO B 240 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 240 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 240 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 485 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   ASN A 485 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ASN A 485 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 486 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 182 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   THR B 182 "    0.039 2.00e-02 2.50e+03
        pdb=" O   THR B 182 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS B 183 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1326 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2113
        2.82 -     3.34: 6615
        3.34 -     3.86: 11465
        3.86 -     4.38: 12880
        4.38 -     4.90: 23012
  Nonbonded interactions: 56085
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 656 "
            pdb=" OE1 GLN B 671 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" NE2 HIS B 606 "
            pdb=" OE1 GLN B 666 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OH  TYR B  39 "
            pdb=" OD1 ASP B 140 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   PRO A 373 "
            pdb=" NE2 GLN A 507 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" NZ  LYS A 113 "
            pdb=" OE2 GLU A 117 "
     model   vdw
     2.364 3.120
  ... (remaining 56080 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.330
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
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      :  0.002   0.035   7780  Z= 0.123
  Angle     :  0.514  11.130  10541  Z= 0.287
  Chirality :  0.038   0.349   1193
  Planarity :  0.003   0.057   1329
  Dihedral  : 12.811  80.424   2873
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.12 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.45 (0.28), residues: 923
  helix:  1.52 (0.25), residues: 449
  sheet:  1.31 (0.38), residues: 177
  loop : -0.03 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 385 
 TYR   0.012   0.001   TYR B 119 
 PHE   0.011   0.001   PHE A 486 
 TRP   0.020   0.001   TRP B  15 
 HIS   0.003   0.000   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7779)
  covalent geometry    : angle       0.51358 (10539)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.89287 (    2)
  hydrogen bonds       : bond        0.23289 (  421)
  hydrogen bonds       : angle       7.05972 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 222
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6630 (mm-30)
REVERT: A  242 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7955 (tp40)
REVERT: A  433 ASP cc_start: 0.7858 (p0) cc_final: 0.7405 (p0)
REVERT: A  475 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7379 (ttmm)
REVERT: A  476 ARG cc_start: 0.7301 (mtm110) cc_final: 0.7040 (mtm110)
REVERT: A  518 LYS cc_start: 0.7417 (tmtt) cc_final: 0.7170 (tmtt)
REVERT: A  619 MET cc_start: 0.6650 (tpt) cc_final: 0.6269 (tpt)
REVERT: B  140 ASP cc_start: 0.6832 (m-30) cc_final: 0.6412 (m-30)
REVERT: B  145 GLN cc_start: 0.7137 (tt0) cc_final: 0.6919 (tt0)
REVERT: B  244 GLN cc_start: 0.5824 (mp10) cc_final: 0.5466 (mp10)
REVERT: B  627 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7003 (mtt180)
REVERT: B  671 GLN cc_start: 0.7356 (tt0) cc_final: 0.7096 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 224
  average time/residue: 0.1245
  time to fit residues: 34.8579
Evaluate side-chains
  194 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  542 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS
A 503 GLN
A 683 GLN
B 158 ASN
B 671 GLN
B 686 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.165778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135891 restraints weight = 10797.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.72
r_work: 0.3587 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7780  Z= 0.172
  Angle     :  0.618   6.653  10541  Z= 0.319
  Chirality :  0.043   0.284   1193
  Planarity :  0.004   0.045   1329
  Dihedral  :  3.852  37.302   1026
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.13 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.62 (0.28), residues: 923
  helix:  1.69 (0.25), residues: 444
  sheet:  1.56 (0.39), residues: 172
  loop : -0.05 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 350 
 TYR   0.018   0.002   TYR B 119 
 PHE   0.023   0.002   PHE A 220 
 TRP   0.017   0.002   TRP B  15 
 HIS   0.012   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7779)
  covalent geometry    : angle       0.61811 (10539)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.82974 (    2)
  hydrogen bonds       : bond        0.05974 (  421)
  hydrogen bonds       : angle       4.99737 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLN cc_start: 0.7174 (tp40) cc_final: 0.6938 (mm110)
REVERT: A   63 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7073 (mm-30)
REVERT: A  204 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6937 (mm-30)
REVERT: A  245 TYR cc_start: 0.8251 (m-80) cc_final: 0.8026 (m-80)
REVERT: A  433 ASP cc_start: 0.7991 (p0) cc_final: 0.7554 (p0)
REVERT: A  619 MET cc_start: 0.7641 (tpt) cc_final: 0.7075 (tpt)
REVERT: B   16 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7433 (m-40)
REVERT: B   22 ASP cc_start: 0.7977 (t0) cc_final: 0.7732 (t0)
REVERT: B   41 TYR cc_start: 0.7683 (t80) cc_final: 0.7462 (t80)
REVERT: B   51 GLU cc_start: 0.7302 (tt0) cc_final: 0.7032 (tt0)
REVERT: B  138 GLU cc_start: 0.8003 (tt0) cc_final: 0.7798 (tt0)
REVERT: B  144 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7339 (tt0)
REVERT: B  244 GLN cc_start: 0.6166 (mp10) cc_final: 0.5637 (mp10)
REVERT: B  671 GLN cc_start: 0.8085 (tt0) cc_final: 0.7389 (tt0)
  outliers start: 14
  outliers final: 6
  residues processed: 211
  average time/residue: 0.1264
  time to fit residues: 33.1980
Evaluate side-chains
  198 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
A 603 GLN
A 683 GLN
B 542 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.159025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.129398 restraints weight = 10627.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.62
r_work: 0.3523 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7780  Z= 0.208
  Angle     :  0.601   7.024  10541  Z= 0.314
  Chirality :  0.042   0.179   1193
  Planarity :  0.004   0.037   1329
  Dihedral  :  3.962  17.574   1024
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.23 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.50 (0.28), residues: 923
  helix:  1.64 (0.25), residues: 450
  sheet:  1.46 (0.39), residues: 172
  loop : -0.21 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 663 
 TYR   0.017   0.002   TYR A 221 
 PHE   0.018   0.002   PHE A 210 
 TRP   0.017   0.002   TRP A 614 
 HIS   0.012   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7779)
  covalent geometry    : angle       0.60115 (10539)
  SS BOND              : bond        0.00588 (    1)
  SS BOND              : angle       1.23260 (    2)
  hydrogen bonds       : bond        0.06452 (  421)
  hydrogen bonds       : angle       4.74126 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8518 (t) cc_final: 0.8282 (p)
REVERT: A   63 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7112 (mm-30)
REVERT: A   75 GLU cc_start: 0.7285 (pm20) cc_final: 0.6993 (pm20)
REVERT: A  163 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6609 (mm-30)
REVERT: A  406 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7078 (mt-10)
REVERT: A  433 ASP cc_start: 0.7983 (p0) cc_final: 0.7583 (p0)
REVERT: A  526 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6806 (ttp80)
REVERT: A  619 MET cc_start: 0.7818 (tpt) cc_final: 0.7475 (tpt)
REVERT: A  663 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7755 (mtp180)
REVERT: B   22 ASP cc_start: 0.8011 (t0) cc_final: 0.7784 (t0)
REVERT: B  111 GLN cc_start: 0.7395 (mt0) cc_final: 0.7104 (mt0)
REVERT: B  138 GLU cc_start: 0.7859 (tt0) cc_final: 0.7633 (tt0)
REVERT: B  244 GLN cc_start: 0.6183 (mp10) cc_final: 0.5611 (mp10)
REVERT: B  636 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (mtp)
REVERT: B  639 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7474 (tm-30)
REVERT: B  665 ILE cc_start: 0.8386 (mm) cc_final: 0.8012 (mt)
  outliers start: 17
  outliers final: 9
  residues processed: 203
  average time/residue: 0.1203
  time to fit residues: 30.2559
Evaluate side-chains
  203 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 193
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.161193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.131266 restraints weight = 10692.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.65
r_work: 0.3515 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7780  Z= 0.172
  Angle     :  0.559   6.468  10541  Z= 0.290
  Chirality :  0.041   0.161   1193
  Planarity :  0.004   0.039   1329
  Dihedral  :  3.909  17.106   1024
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.18 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.52 (0.28), residues: 923
  helix:  1.76 (0.25), residues: 445
  sheet:  1.40 (0.40), residues: 172
  loop : -0.31 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 349 
 TYR   0.024   0.002   TYR B 119 
 PHE   0.017   0.002   PHE A 210 
 TRP   0.017   0.002   TRP B  92 
 HIS   0.010   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7779)
  covalent geometry    : angle       0.55857 (10539)
  SS BOND              : bond        0.00499 (    1)
  SS BOND              : angle       1.54157 (    2)
  hydrogen bonds       : bond        0.05389 (  421)
  hydrogen bonds       : angle       4.57756 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8516 (t) cc_final: 0.8268 (p)
REVERT: A   63 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7045 (mm-30)
REVERT: A   75 GLU cc_start: 0.7376 (pm20) cc_final: 0.7138 (pm20)
REVERT: A  433 ASP cc_start: 0.7945 (p0) cc_final: 0.7535 (p0)
REVERT: A  469 GLN cc_start: 0.7418 (mp-120) cc_final: 0.6877 (mp10)
REVERT: A  526 ARG cc_start: 0.7047 (tpp80) cc_final: 0.6834 (ttp80)
REVERT: A  619 MET cc_start: 0.7815 (tpt) cc_final: 0.7469 (tpt)
REVERT: B   22 ASP cc_start: 0.7958 (t0) cc_final: 0.7752 (t0)
REVERT: B  138 GLU cc_start: 0.7698 (tt0) cc_final: 0.7485 (tt0)
REVERT: B  140 ASP cc_start: 0.7912 (t0) cc_final: 0.7644 (t0)
REVERT: B  145 GLN cc_start: 0.8291 (tt0) cc_final: 0.8088 (tt0)
REVERT: B  636 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (mtp)
REVERT: B  639 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7366 (tm-30)
REVERT: B  665 ILE cc_start: 0.8380 (mm) cc_final: 0.8006 (mt)
  outliers start: 23
  outliers final: 12
  residues processed: 196
  average time/residue: 0.1043
  time to fit residues: 25.7771
Evaluate side-chains
  191 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0070
   chunk 51 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 158 ASN
B 244 GLN
B 666 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.159881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.130323 restraints weight = 10578.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.63
r_work: 0.3541 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7780  Z= 0.113
  Angle     :  0.521  10.549  10541  Z= 0.265
  Chirality :  0.039   0.141   1193
  Planarity :  0.004   0.044   1329
  Dihedral  :  3.742  15.551   1024
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.45 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.75 (0.29), residues: 923
  helix:  2.00 (0.25), residues: 445
  sheet:  1.45 (0.40), residues: 172
  loop : -0.25 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 160 
 TYR   0.028   0.001   TYR A 221 
 PHE   0.014   0.001   PHE A 210 
 TRP   0.013   0.001   TRP B  92 
 HIS   0.008   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7779)
  covalent geometry    : angle       0.52088 (10539)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       1.23061 (    2)
  hydrogen bonds       : bond        0.04361 (  421)
  hydrogen bonds       : angle       4.41896 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7063 (mm-30)
REVERT: A   67 ASP cc_start: 0.7499 (m-30) cc_final: 0.7203 (m-30)
REVERT: A  433 ASP cc_start: 0.7935 (p0) cc_final: 0.7518 (p0)
REVERT: A  619 MET cc_start: 0.7780 (tpt) cc_final: 0.7435 (tpt)
REVERT: B  111 GLN cc_start: 0.7453 (mt0) cc_final: 0.7174 (mm-40)
REVERT: B  244 GLN cc_start: 0.6203 (mm-40) cc_final: 0.5979 (mm110)
REVERT: B  636 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8231 (mtp)
REVERT: B  639 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7356 (tm-30)
REVERT: B  665 ILE cc_start: 0.8344 (mm) cc_final: 0.7959 (mt)
REVERT: B  666 GLN cc_start: 0.7737 (pt0) cc_final: 0.7492 (pt0)
  outliers start: 20
  outliers final: 13
  residues processed: 192
  average time/residue: 0.1134
  time to fit residues: 27.2780
Evaluate side-chains
  196 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.159455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.129765 restraints weight = 10678.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.64
r_work: 0.3528 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7780  Z= 0.134
  Angle     :  0.528   7.134  10541  Z= 0.269
  Chirality :  0.039   0.134   1193
  Planarity :  0.004   0.044   1329
  Dihedral  :  3.722  15.480   1024
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.81 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.78 (0.29), residues: 923
  helix:  2.05 (0.25), residues: 445
  sheet:  1.47 (0.40), residues: 172
  loop : -0.27 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 160 
 TYR   0.020   0.001   TYR A 221 
 PHE   0.016   0.002   PHE A 210 
 TRP   0.012   0.001   TRP A 614 
 HIS   0.007   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7779)
  covalent geometry    : angle       0.52737 (10539)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       1.32143 (    2)
  hydrogen bonds       : bond        0.04571 (  421)
  hydrogen bonds       : angle       4.36373 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7073 (mm-30)
REVERT: A  433 ASP cc_start: 0.7948 (p0) cc_final: 0.7525 (p0)
REVERT: A  526 ARG cc_start: 0.7019 (ttp80) cc_final: 0.6789 (ttp80)
REVERT: A  619 MET cc_start: 0.7807 (tpt) cc_final: 0.7459 (tpt)
REVERT: B  150 THR cc_start: 0.6782 (m) cc_final: 0.6531 (m)
REVERT: B  156 ILE cc_start: 0.8191 (mm) cc_final: 0.7928 (mt)
REVERT: B  244 GLN cc_start: 0.6226 (mm-40) cc_final: 0.5779 (mp10)
REVERT: B  542 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7894 (t0)
REVERT: B  631 GLN cc_start: 0.7680 (mt0) cc_final: 0.7373 (mt0)
REVERT: B  636 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (mtp)
REVERT: B  639 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7369 (tm-30)
REVERT: B  665 ILE cc_start: 0.8368 (mm) cc_final: 0.7986 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 193
  average time/residue: 0.0965
  time to fit residues: 23.4544
Evaluate side-chains
  198 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  542 ASN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0010
   chunk 10 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 683 GLN
B  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.159148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.129495 restraints weight = 10616.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.64
r_work: 0.3529 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7780  Z= 0.132
  Angle     :  0.526   7.223  10541  Z= 0.267
  Chirality :  0.039   0.193   1193
  Planarity :  0.004   0.044   1329
  Dihedral  :  3.712  15.475   1024
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.76 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.81 (0.29), residues: 923
  helix:  2.12 (0.25), residues: 444
  sheet:  1.45 (0.39), residues: 172
  loop : -0.30 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 160 
 TYR   0.016   0.001   TYR A 221 
 PHE   0.016   0.001   PHE A 210 
 TRP   0.012   0.001   TRP B  92 
 HIS   0.005   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7779)
  covalent geometry    : angle       0.52530 (10539)
  SS BOND              : bond        0.00307 (    1)
  SS BOND              : angle       1.34799 (    2)
  hydrogen bonds       : bond        0.04529 (  421)
  hydrogen bonds       : angle       4.32691 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7075 (mm-30)
REVERT: A  433 ASP cc_start: 0.7959 (p0) cc_final: 0.7538 (p0)
REVERT: A  526 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6797 (ttp80)
REVERT: A  619 MET cc_start: 0.7772 (tpt) cc_final: 0.7437 (tpt)
REVERT: B  144 GLU cc_start: 0.8185 (tt0) cc_final: 0.7820 (tm-30)
REVERT: B  150 THR cc_start: 0.6740 (m) cc_final: 0.6483 (m)
REVERT: B  156 ILE cc_start: 0.8229 (mm) cc_final: 0.7965 (mt)
REVERT: B  197 LYS cc_start: 0.8316 (mttm) cc_final: 0.7864 (mttm)
REVERT: B  244 GLN cc_start: 0.6267 (mm-40) cc_final: 0.5821 (mp10)
REVERT: B  542 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7879 (t0)
REVERT: B  631 GLN cc_start: 0.7652 (mt0) cc_final: 0.7313 (mt0)
REVERT: B  636 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8276 (mtp)
REVERT: B  639 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7371 (tm-30)
REVERT: B  665 ILE cc_start: 0.8271 (mm) cc_final: 0.7884 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 193
  average time/residue: 0.1112
  time to fit residues: 27.1321
Evaluate side-chains
  203 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 187
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  119 TYR
Chi-restraints excluded: chain B residue  184 GLN
Chi-restraints excluded: chain B residue  542 ASN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.157827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.128214 restraints weight = 10556.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.61
r_work: 0.3513 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7780  Z= 0.167
  Angle     :  0.554   8.173  10541  Z= 0.282
  Chirality :  0.040   0.125   1193
  Planarity :  0.004   0.042   1329
  Dihedral  :  3.795  15.761   1024
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.36 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.75 (0.29), residues: 923
  helix:  2.09 (0.25), residues: 444
  sheet:  1.36 (0.39), residues: 174
  loop : -0.35 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 349 
 TYR   0.014   0.001   TYR A 221 
 PHE   0.018   0.002   PHE A 210 
 TRP   0.048   0.002   TRP B 161 
 HIS   0.006   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7779)
  covalent geometry    : angle       0.55324 (10539)
  SS BOND              : bond        0.00444 (    1)
  SS BOND              : angle       1.56696 (    2)
  hydrogen bonds       : bond        0.05020 (  421)
  hydrogen bonds       : angle       4.38062 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7116 (mm-30)
REVERT: A  163 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6619 (mm-30)
REVERT: A  433 ASP cc_start: 0.7967 (p0) cc_final: 0.7538 (p0)
REVERT: A  526 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6852 (ttp80)
REVERT: A  619 MET cc_start: 0.7763 (tpt) cc_final: 0.7439 (tpt)
REVERT: A  651 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7770 (mtp180)
REVERT: B  144 GLU cc_start: 0.8178 (tt0) cc_final: 0.7848 (tm-30)
REVERT: B  156 ILE cc_start: 0.8313 (mm) cc_final: 0.8085 (mt)
REVERT: B  197 LYS cc_start: 0.8289 (mttm) cc_final: 0.7807 (mttm)
REVERT: B  244 GLN cc_start: 0.6272 (mm-40) cc_final: 0.5832 (mp10)
REVERT: B  631 GLN cc_start: 0.7686 (mt0) cc_final: 0.7350 (mt0)
REVERT: B  636 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8307 (mtp)
REVERT: B  639 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7335 (tm-30)
REVERT: B  665 ILE cc_start: 0.8350 (mm) cc_final: 0.7963 (mt)
REVERT: B  671 GLN cc_start: 0.8253 (tt0) cc_final: 0.7871 (tt0)
  outliers start: 17
  outliers final: 11
  residues processed: 194
  average time/residue: 0.1120
  time to fit residues: 27.2030
Evaluate side-chains
  201 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 189
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.158413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128683 restraints weight = 10508.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.61
r_work: 0.3518 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7780  Z= 0.157
  Angle     :  0.559   8.188  10541  Z= 0.285
  Chirality :  0.040   0.144   1193
  Planarity :  0.004   0.040   1329
  Dihedral  :  3.828  16.156   1024
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.12 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.77 (0.29), residues: 923
  helix:  2.17 (0.25), residues: 444
  sheet:  1.33 (0.39), residues: 168
  loop : -0.38 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 349 
 TYR   0.028   0.001   TYR A 221 
 PHE   0.017   0.002   PHE A 210 
 TRP   0.032   0.002   TRP B 161 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7779)
  covalent geometry    : angle       0.55882 (10539)
  SS BOND              : bond        0.00428 (    1)
  SS BOND              : angle       1.52695 (    2)
  hydrogen bonds       : bond        0.04956 (  421)
  hydrogen bonds       : angle       4.40525 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7126 (mm-30)
REVERT: A  163 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6596 (mm-30)
REVERT: A  433 ASP cc_start: 0.7970 (p0) cc_final: 0.7542 (p0)
REVERT: A  526 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6846 (ttp80)
REVERT: A  619 MET cc_start: 0.7799 (tpt) cc_final: 0.7479 (tpt)
REVERT: A  651 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7756 (mtp180)
REVERT: B  144 GLU cc_start: 0.8181 (tt0) cc_final: 0.7860 (tm-30)
REVERT: B  156 ILE cc_start: 0.8328 (mm) cc_final: 0.8125 (mt)
REVERT: B  197 LYS cc_start: 0.8286 (mttm) cc_final: 0.7826 (mttm)
REVERT: B  244 GLN cc_start: 0.6326 (mm-40) cc_final: 0.5851 (mp10)
REVERT: B  631 GLN cc_start: 0.7676 (mt0) cc_final: 0.7325 (mt0)
REVERT: B  636 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8330 (mtp)
REVERT: B  639 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7312 (tm-30)
REVERT: B  665 ILE cc_start: 0.8347 (mm) cc_final: 0.7958 (mt)
REVERT: B  671 GLN cc_start: 0.8275 (tt0) cc_final: 0.7840 (tt0)
  outliers start: 17
  outliers final: 15
  residues processed: 197
  average time/residue: 0.0997
  time to fit residues: 24.9972
Evaluate side-chains
  205 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 189
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  184 GLN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 88 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.158836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128809 restraints weight = 10521.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.63
r_work: 0.3525 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7780  Z= 0.143
  Angle     :  0.549   8.522  10541  Z= 0.279
  Chirality :  0.040   0.148   1193
  Planarity :  0.004   0.041   1329
  Dihedral  :  3.798  15.943   1024
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.83 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.84 (0.29), residues: 923
  helix:  2.21 (0.25), residues: 444
  sheet:  1.36 (0.39), residues: 168
  loop : -0.30 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  27 
 TYR   0.024   0.001   TYR A 221 
 PHE   0.016   0.001   PHE A 210 
 TRP   0.013   0.002   TRP B  92 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7779)
  covalent geometry    : angle       0.54912 (10539)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       1.41842 (    2)
  hydrogen bonds       : bond        0.04678 (  421)
  hydrogen bonds       : angle       4.37966 ( 1233)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.8491 (t) cc_final: 0.8234 (p)
REVERT: A   63 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7101 (mm-30)
REVERT: A  406 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6998 (mt-10)
REVERT: A  433 ASP cc_start: 0.8007 (p0) cc_final: 0.7578 (p0)
REVERT: A  469 GLN cc_start: 0.7311 (mp-120) cc_final: 0.7063 (mp10)
REVERT: A  526 ARG cc_start: 0.7097 (ttp80) cc_final: 0.6858 (ttp80)
REVERT: A  619 MET cc_start: 0.7804 (tpt) cc_final: 0.7478 (tpt)
REVERT: A  651 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7793 (mtp180)
REVERT: B  144 GLU cc_start: 0.8166 (tt0) cc_final: 0.7887 (tm-30)
REVERT: B  197 LYS cc_start: 0.8271 (mttm) cc_final: 0.7823 (mttm)
REVERT: B  244 GLN cc_start: 0.6351 (mm-40) cc_final: 0.5848 (mp10)
REVERT: B  631 GLN cc_start: 0.7675 (mt0) cc_final: 0.7337 (mt0)
REVERT: B  636 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8314 (mtp)
REVERT: B  639 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7312 (tm-30)
REVERT: B  665 ILE cc_start: 0.8278 (mm) cc_final: 0.7883 (mt)
REVERT: B  671 GLN cc_start: 0.8274 (tt0) cc_final: 0.8062 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 200
  average time/residue: 0.0970
  time to fit residues: 24.5430
Evaluate side-chains
  209 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 195
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  410 LYS
Chi-restraints excluded: chain A residue  554 MET
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain B residue   15 TRP
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  184 GLN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  601 THR
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  661 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0470
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 71 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 72 optimal weight:    7.9990
   chunk 49 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.4278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.160006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.130249 restraints weight = 10491.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.62
r_work: 0.3543 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7780  Z= 0.112
  Angle     :  0.530   8.861  10541  Z= 0.268
  Chirality :  0.039   0.148   1193
  Planarity :  0.004   0.042   1329
  Dihedral  :  3.691  14.761   1024
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.59 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.98 (0.29), residues: 923
  helix:  2.33 (0.25), residues: 444
  sheet:  1.42 (0.39), residues: 167
  loop : -0.24 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  27 
 TYR   0.027   0.001   TYR A 221 
 PHE   0.018   0.001   PHE A 220 
 TRP   0.013   0.001   TRP B  92 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7779)
  covalent geometry    : angle       0.52966 (10539)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.34587 (    2)
  hydrogen bonds       : bond        0.04119 (  421)
  hydrogen bonds       : angle       4.30837 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1624.35 seconds
wall clock time: 28 minutes 31.41 seconds (1711.41 seconds total)