Starting phenix.real_space_refine
on Tue Feb  3 17:20:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9shq_54908/02_2026/9shq_54908.map"
  }
  resolution = 4.2
  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=   0.003 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    3428      2.51       5
     N     945      2.21       5
     O     999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  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: 5409
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 5285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 5285
          Classifications: {'peptide': 661}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 30, 'TRANS': 630}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 88
          Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 3, 'TRP:plan': 3}
          Unresolved non-hydrogen planarities: 76
    Chain: "C"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Classifications: {'RNA': 3}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 1, 'rna3p': 1}
    Chain: "D"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'RNA': 3}
          Modifications used: {'rna2p_pyr': 3}
          Link IDs: {'rna2p': 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.35, per 1000 atoms: 0.25
  Number of scatterers: 5409
  At special positions: 0
  Unit cell: (83, 111.22, 84.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     Mg      1     11.99
     O     999      8.00
     N     945      7.00
     C    3428      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 375.8 milliseconds
  

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      35.6% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 145 through 150
      removed outlier: 3.690A  pdb=" N   SER B 148 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 224
      removed outlier: 3.684A  pdb=" N   ASN B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET B 224 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 289
      removed outlier: 3.785A  pdb=" N   PHE B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.709A  pdb=" N   GLU B 303 " --> pdb=" O   GLN B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 412
      removed outlier: 4.441A  pdb=" N   HIS B 410 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 432
      removed outlier: 3.724A  pdb=" N   LEU B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 443
      removed outlier: 4.302A  pdb=" N   GLN B 436 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG B 437 " --> pdb=" O   ASP B 433 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU B 438 " --> pdb=" O   ASN B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 484
      removed outlier: 3.606A  pdb=" N   ARG B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 524
      removed outlier: 3.553A  pdb=" N   PHE B 517 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
      Proline residue:  B 521  - end of helix
    Processing helix  chain 'B' and resid 538 through 550
      removed outlier: 3.802A  pdb=" N   LEU B 543 " --> pdb=" O   THR B 539 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG B 544 " --> pdb=" O   GLU B 540 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA B 545 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU B 546 " --> pdb=" O   TYR B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 579
      removed outlier: 3.653A  pdb=" N   TYR B 569 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 593
    Processing helix  chain 'B' and resid 597 through 613
      removed outlier: 3.552A  pdb=" N   LYS B 604 " --> pdb=" O   ALA B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 691
      removed outlier: 3.770A  pdb=" N   LYS B 677 " --> pdb=" O   VAL B 673 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL B 678 " --> pdb=" O   ASP B 674 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 684 " --> pdb=" O   LEU B 680 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ARG B 685 " --> pdb=" O   GLN B 681 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER B 688 " --> pdb=" O   LEU B 684 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLY B 689 " --> pdb=" O   ARG B 685 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   CYS B 690 " --> pdb=" O   ALA B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 716
      removed outlier: 3.668A  pdb=" N   VAL B 714 " --> pdb=" O   LEU B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 725
    Processing helix  chain 'B' and resid 806 through 817
      removed outlier: 3.628A  pdb=" N   ARG B 811 " --> pdb=" O   ASP B 807 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR B 813 " --> pdb=" O   ILE B 809 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   TYR B 814 " --> pdb=" O   GLN B 810 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LYS B 815 " --> pdb=" O   ARG B 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 846
    Processing helix  chain 'B' and resid 854 through 858
      removed outlier: 4.138A  pdb=" N   ASN B 857 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 164
      removed outlier: 3.698A  pdb=" N   ALA B 163 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE B 170 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 169 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLN B 132 " --> pdb=" O   ASN B 200 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASN B 200 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   HIS B 134 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU B 198 " --> pdb=" O   HIS B 134 " (cutoff:3.500A)
      removed outlier: 8.546A  pdb=" N   ASP B 136 " --> pdb=" O   ILE B 196 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B 196 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 227 through 229
    Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 242
      removed outlier: 3.501A  pdb=" N   VAL B 248 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 259
      removed outlier: 3.788A  pdb=" N   LEU B 258 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 319
      removed outlier: 3.866A  pdb=" N   ILE B 308 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR B 389 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 456 through 457
      removed outlier: 3.786A  pdb=" N   ARG B 456 " --> pdb=" O   VAL B 765 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE B 798 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 798 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ASP B 800 " --> pdb=" O   LEU B 736 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU B 736 " --> pdb=" O   ASP B 800 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR B 737 " --> pdb=" O   VAL B 698 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   MET B 628 " --> pdb=" O   ILE B 699 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   TYR B 701 " --> pdb=" O   MET B 628 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL B 630 " --> pdb=" O   TYR B 701 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   ASP B 703 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE B 632 " --> pdb=" O   ASP B 703 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   ILE B 629 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 531 through 533
      removed outlier: 7.897A  pdb=" N   TRP B 497 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   ILE B 533 " --> pdb=" O   TRP B 497 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU B 499 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 498 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL B 558 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLN B 585 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS B 559 " --> pdb=" O   GLN B 585 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 587 " --> pdb=" O   CYS B 559 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 751 through 753
      removed outlier: 4.717A  pdb=" N   ALA B 751 " --> pdb=" O   GLN B 758 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLN B 758 " --> pdb=" O   ALA B 751 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER B 753 " --> pdb=" O   ARG B 756 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 756 " --> pdb=" O   SER B 753 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    182 hydrogen bonds defined for protein.
    507 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: 0.73

  Time building geometry restraints manager: 0.51 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: 1748
        1.34 -     1.46: 1261
        1.46 -     1.58: 2466
        1.58 -     1.70: 10
        1.70 -     1.82: 45
  Bond restraints: 5530
  Sorted by residual:
  bond pdb=" O5'   A C   3 "
       pdb=" C5'   A C   3 "
    ideal  model  delta    sigma   weight residual
    1.420  1.451 -0.031 1.50e-02 4.44e+03 4.30e+00
  bond pdb=" O5'   U D   2 "
       pdb=" C5'   U D   2 "
    ideal  model  delta    sigma   weight residual
    1.424  1.453 -0.029 1.50e-02 4.44e+03 3.83e+00
  bond pdb=" O5'   U C   2 "
       pdb=" C5'   U C   2 "
    ideal  model  delta    sigma   weight residual
    1.420  1.447 -0.027 1.50e-02 4.44e+03 3.32e+00
  bond pdb=" O5'   C D   3 "
       pdb=" C5'   C D   3 "
    ideal  model  delta    sigma   weight residual
    1.424  1.451 -0.027 1.50e-02 4.44e+03 3.26e+00
  bond pdb=" P     U C   1 "
       pdb=" OP3   U C   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.516 -0.036 2.00e-02 2.50e+03 3.20e+00
  ... (remaining 5525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 7408
        2.52 -     5.03: 98
        5.03 -     7.55: 14
        7.55 -    10.07: 2
       10.07 -    12.58: 1
  Bond angle restraints: 7523
  Sorted by residual:
  angle pdb=" CA  LEU B 626 "
        pdb=" CB  LEU B 626 "
        pdb=" CG  LEU B 626 "
      ideal   model   delta    sigma   weight residual
     116.30  128.88  -12.58 3.50e+00 8.16e-02 1.29e+01
  angle pdb=" C4'   U C   2 "
        pdb=" C3'   U C   2 "
        pdb=" O3'   U C   2 "
      ideal   model   delta    sigma   weight residual
     113.00  108.11    4.89 1.50e+00 4.44e-01 1.06e+01
  angle pdb=" C   ASN B 715 "
        pdb=" N   TYR B 716 "
        pdb=" CA  TYR B 716 "
      ideal   model   delta    sigma   weight residual
     121.54  115.49    6.05 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" CA  PRO B 203 "
        pdb=" N   PRO B 203 "
        pdb=" CD  PRO B 203 "
      ideal   model   delta    sigma   weight residual
     112.00  107.68    4.32 1.40e+00 5.10e-01 9.50e+00
  angle pdb=" CA  LEU B 812 "
        pdb=" CB  LEU B 812 "
        pdb=" CG  LEU B 812 "
      ideal   model   delta    sigma   weight residual
     116.30  125.83   -9.53 3.50e+00 8.16e-02 7.41e+00
  ... (remaining 7518 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.12: 3261
       34.12 -    68.24: 69
       68.24 -   102.36: 9
      102.36 -   136.47: 2
      136.47 -   170.59: 1
  Dihedral angle restraints: 3342
    sinusoidal: 1402
      harmonic: 1940
  Sorted by residual:
  dihedral pdb=" O4'   U D   2 "
           pdb=" C1'   U D   2 "
           pdb=" N1    U D   2 "
           pdb=" C2    U D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   42.59 -170.59     1      1.70e+01 3.46e-03 6.60e+01
  dihedral pdb=" O4'   C D   3 "
           pdb=" C1'   C D   3 "
           pdb=" N1    C D   3 "
           pdb=" C2    C D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -39.91  -88.09     1      1.70e+01 3.46e-03 3.21e+01
  dihedral pdb=" C4'   C D   3 "
           pdb=" O4'   C D   3 "
           pdb=" C1'   C D   3 "
           pdb=" C2'   C D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -21.00   10.12  -31.12     1      8.00e+00 1.56e-02 2.16e+01
  ... (remaining 3339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 832
       0.115 -    0.230: 23
       0.230 -    0.345: 1
       0.345 -    0.460: 2
       0.460 -    0.575: 4
  Chirality restraints: 862
  Sorted by residual:
  chirality pdb=" P     C D   1 "
            pdb=" OP1   C D   1 "
            pdb=" OP2   C D   1 "
            pdb=" O5'   C D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.99   -0.57 2.00e-01 2.50e+01 8.26e+00
  chirality pdb=" P     U C   1 "
            pdb=" OP1   U C   1 "
            pdb=" OP2   U C   1 "
            pdb=" O5'   U C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.96   -0.55 2.00e-01 2.50e+01 7.53e+00
  chirality pdb=" P     U D   2 "
            pdb=" OP1   U D   2 "
            pdb=" OP2   U D   2 "
            pdb=" O5'   U D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.89   -0.48 2.00e-01 2.50e+01 5.66e+00
  ... (remaining 859 not shown)

  Planarity restraints: 939
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 202 "   -0.085 5.00e-02 4.00e+02   1.27e-01 2.60e+01
        pdb=" N   PRO B 203 "    0.220 5.00e-02 4.00e+02
        pdb=" CA  PRO B 203 "   -0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO B 203 "   -0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 829 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO B 830 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 830 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 830 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 384 "    0.028 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO B 385 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 385 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 385 "    0.023 5.00e-02 4.00e+02
  ... (remaining 936 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 29
        2.35 -     2.99: 2690
        2.99 -     3.62: 8373
        3.62 -     4.26: 11681
        4.26 -     4.90: 18621
  Nonbonded interactions: 41394
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 585 "
            pdb=" OXT LEU B 862 "
     model   vdw
     1.710 3.040
  nonbonded pdb=" NE2 GLN B 585 "
            pdb="MG    MG B 901 "
     model   vdw
     1.895 2.250
  nonbonded pdb=" CD  GLN B 585 "
            pdb="MG    MG B 901 "
     model   vdw
     2.074 2.400
  nonbonded pdb=" OE1 GLN B 585 "
            pdb="MG    MG B 901 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O   LEU B 862 "
            pdb="MG    MG B 901 "
     model   vdw
     2.102 2.170
  ... (remaining 41389 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.090
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5530  Z= 0.173
  Angle     :  0.720  12.584   7523  Z= 0.363
  Chirality :  0.063   0.575    862
  Planarity :  0.006   0.127    939
  Dihedral  : 15.687 170.592   2088
  Min Nonbonded Distance : 1.710

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.32), residues: 649
  helix: -0.13 (0.39), residues: 172
  sheet:  0.02 (0.47), residues: 114
  loop : -1.23 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 538 
 TYR   0.017   0.001   TYR B 428 
 PHE   0.013   0.001   PHE B 517 
 TRP   0.014   0.001   TRP B 618 
 HIS   0.007   0.001   HIS B 794 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5530)
  covalent geometry    : angle       0.72034 ( 7523)
  hydrogen bonds       : bond        0.30401 (  182)
  hydrogen bonds       : angle       9.44578 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 THR cc_start: 0.7991 (p) cc_final: 0.7636 (p)
REVERT: B  265 MET cc_start: 0.5819 (mmt) cc_final: 0.5603 (mmm)
REVERT: B  414 THR cc_start: 0.9628 (p) cc_final: 0.9322 (t)
REVERT: B  416 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7855 (mm-30)
REVERT: B  417 GLN cc_start: 0.9211 (mt0) cc_final: 0.8676 (tt0)
REVERT: B  599 MET cc_start: 0.9101 (tmm) cc_final: 0.8840 (tmm)
REVERT: B  746 ASN cc_start: 0.8462 (p0) cc_final: 0.7950 (p0)
REVERT: B  833 CYS cc_start: 0.9298 (m) cc_final: 0.8926 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0659
  time to fit residues: 7.7144
Evaluate side-chains
  66 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 177 HIS
B 610 ASN
B 810 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.080516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.067176 restraints weight = 31445.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.069017 restraints weight = 21732.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.070408 restraints weight = 16321.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.071474 restraints weight = 12949.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.072306 restraints weight = 10729.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5530  Z= 0.149
  Angle     :  0.580  11.118   7523  Z= 0.302
  Chirality :  0.044   0.174    862
  Planarity :  0.005   0.081    939
  Dihedral  : 13.581 179.607    816
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.31), residues: 649
  helix: -0.32 (0.35), residues: 201
  sheet: -0.03 (0.47), residues: 117
  loop : -1.63 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 538 
 TYR   0.015   0.002   TYR B 575 
 PHE   0.020   0.002   PHE B 517 
 TRP   0.009   0.001   TRP B 618 
 HIS   0.005   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5530)
  covalent geometry    : angle       0.58000 ( 7523)
  hydrogen bonds       : bond        0.05284 (  182)
  hydrogen bonds       : angle       6.84505 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  414 THR cc_start: 0.9564 (p) cc_final: 0.9194 (t)
REVERT: B  417 GLN cc_start: 0.8963 (mt0) cc_final: 0.8196 (tt0)
REVERT: B  419 GLN cc_start: 0.9206 (pp30) cc_final: 0.9005 (pp30)
REVERT: B  599 MET cc_start: 0.9185 (tmm) cc_final: 0.8902 (tmm)
REVERT: B  616 GLU cc_start: 0.7387 (mp0) cc_final: 0.7176 (mt-10)
REVERT: B  633 ASP cc_start: 0.8752 (t70) cc_final: 0.8520 (t70)
REVERT: B  703 ASP cc_start: 0.8212 (t70) cc_final: 0.7646 (t70)
REVERT: B  746 ASN cc_start: 0.8537 (p0) cc_final: 0.8080 (p0)
REVERT: B  782 SER cc_start: 0.9373 (p) cc_final: 0.9148 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0548
  time to fit residues: 5.8820
Evaluate side-chains
  62 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 40 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0170
   overall best weight:    2.0422

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

Flipped N/Q/H residues before XYZ refinement:
B 515 ASN
B 759 ASN
B 810 GLN
B 822 ASN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.079444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.066161 restraints weight = 30823.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.067936 restraints weight = 21506.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.069295 restraints weight = 16326.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.070326 restraints weight = 13075.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.071121 restraints weight = 10925.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5530  Z= 0.141
  Angle     :  0.556  10.078   7523  Z= 0.288
  Chirality :  0.043   0.203    862
  Planarity :  0.004   0.067    939
  Dihedral  : 13.597 177.585    816
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.24 (0.31), residues: 649
  helix:  0.02 (0.38), residues: 201
  sheet: -0.20 (0.47), residues: 117
  loop : -1.61 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 538 
 TYR   0.012   0.001   TYR B 542 
 PHE   0.016   0.002   PHE B 517 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.004   0.001   HIS B 794 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5530)
  covalent geometry    : angle       0.55563 ( 7523)
  hydrogen bonds       : bond        0.04219 (  182)
  hydrogen bonds       : angle       6.25794 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 THR cc_start: 0.8188 (p) cc_final: 0.7879 (p)
REVERT: B  269 ASP cc_start: 0.8834 (t0) cc_final: 0.8170 (t0)
REVERT: B  599 MET cc_start: 0.9053 (tmm) cc_final: 0.8740 (tmm)
REVERT: B  633 ASP cc_start: 0.8910 (t70) cc_final: 0.8701 (t70)
REVERT: B  703 ASP cc_start: 0.8165 (t70) cc_final: 0.7684 (t70)
REVERT: B  746 ASN cc_start: 0.8569 (p0) cc_final: 0.8068 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0564
  time to fit residues: 5.8826
Evaluate side-chains
  59 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0870
   chunk 52 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0562

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 232 ASN
B 286 ASN
B 496 ASN
B 548 GLN
B 585 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.080435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.067118 restraints weight = 30488.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.068953 restraints weight = 20920.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.070348 restraints weight = 15687.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.071413 restraints weight = 12469.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.072234 restraints weight = 10327.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5530  Z= 0.103
  Angle     :  0.533   8.943   7523  Z= 0.270
  Chirality :  0.042   0.185    862
  Planarity :  0.004   0.059    939
  Dihedral  : 13.437 178.889    816
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.32), residues: 649
  helix:  0.19 (0.38), residues: 200
  sheet:  0.07 (0.47), residues: 115
  loop : -1.53 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 685 
 TYR   0.010   0.001   TYR B 428 
 PHE   0.015   0.001   PHE B 517 
 TRP   0.007   0.001   TRP B 618 
 HIS   0.003   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 5530)
  covalent geometry    : angle       0.53266 ( 7523)
  hydrogen bonds       : bond        0.03407 (  182)
  hydrogen bonds       : angle       5.86726 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B  244 ASN cc_start: 0.8482 (p0) cc_final: 0.8277 (p0)
REVERT: B  254 THR cc_start: 0.8313 (p) cc_final: 0.7992 (p)
REVERT: B  269 ASP cc_start: 0.8819 (t0) cc_final: 0.8117 (t0)
REVERT: B  419 GLN cc_start: 0.9290 (pp30) cc_final: 0.9063 (pp30)
REVERT: B  599 MET cc_start: 0.8989 (tmm) cc_final: 0.8626 (tmm)
REVERT: B  628 MET cc_start: 0.7776 (tpt) cc_final: 0.7570 (tpt)
REVERT: B  746 ASN cc_start: 0.8549 (p0) cc_final: 0.8040 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0522
  time to fit residues: 5.5566
Evaluate side-chains
  61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 18 optimal weight:    0.2980
   chunk 25 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 ASN
B 834 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.081040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.067580 restraints weight = 31394.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.069447 restraints weight = 21684.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.070834 restraints weight = 16271.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.071871 restraints weight = 12923.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.072683 restraints weight = 10739.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5530  Z= 0.095
  Angle     :  0.555  11.128   7523  Z= 0.272
  Chirality :  0.043   0.209    862
  Planarity :  0.004   0.055    939
  Dihedral  : 13.300 179.206    816
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.31 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.32), residues: 649
  helix:  0.25 (0.38), residues: 200
  sheet: -0.11 (0.46), residues: 115
  loop : -1.47 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 538 
 TYR   0.013   0.001   TYR B 575 
 PHE   0.026   0.002   PHE B 170 
 TRP   0.006   0.001   TRP B 618 
 HIS   0.002   0.000   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 5530)
  covalent geometry    : angle       0.55507 ( 7523)
  hydrogen bonds       : bond        0.03088 (  182)
  hydrogen bonds       : angle       5.54169 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8588 (p0) cc_final: 0.8336 (p0)
REVERT: B  269 ASP cc_start: 0.8774 (t0) cc_final: 0.8067 (t0)
REVERT: B  419 GLN cc_start: 0.9255 (pp30) cc_final: 0.9028 (pp30)
REVERT: B  599 MET cc_start: 0.9000 (tmm) cc_final: 0.8626 (tmm)
REVERT: B  628 MET cc_start: 0.7256 (tpt) cc_final: 0.6905 (tpt)
REVERT: B  746 ASN cc_start: 0.8570 (p0) cc_final: 0.8152 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0567
  time to fit residues: 6.0121
Evaluate side-chains
  55 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 ASN
B 510 ASN
B 548 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.079389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.066120 restraints weight = 31310.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.067889 restraints weight = 21876.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.069219 restraints weight = 16619.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.070224 restraints weight = 13331.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.071021 restraints weight = 11125.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5530  Z= 0.118
  Angle     :  0.563   9.750   7523  Z= 0.282
  Chirality :  0.043   0.231    862
  Planarity :  0.004   0.052    939
  Dihedral  : 13.245 178.520    816
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.47 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.32), residues: 649
  helix:  0.35 (0.38), residues: 201
  sheet: -0.18 (0.47), residues: 116
  loop : -1.43 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 125 
 TYR   0.015   0.001   TYR B 575 
 PHE   0.022   0.002   PHE B 217 
 TRP   0.006   0.001   TRP B 823 
 HIS   0.005   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5530)
  covalent geometry    : angle       0.56336 ( 7523)
  hydrogen bonds       : bond        0.03053 (  182)
  hydrogen bonds       : angle       5.49768 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8551 (p0) cc_final: 0.8243 (p0)
REVERT: B  269 ASP cc_start: 0.8774 (t0) cc_final: 0.8068 (t0)
REVERT: B  419 GLN cc_start: 0.9325 (pp30) cc_final: 0.9096 (pp30)
REVERT: B  507 GLU cc_start: 0.9224 (mp0) cc_final: 0.8737 (pm20)
REVERT: B  599 MET cc_start: 0.9012 (tmm) cc_final: 0.8640 (tmm)
REVERT: B  628 MET cc_start: 0.7377 (tpt) cc_final: 0.7023 (tpt)
REVERT: B  680 LEU cc_start: 0.9763 (tp) cc_final: 0.9557 (tp)
REVERT: B  746 ASN cc_start: 0.8570 (p0) cc_final: 0.8180 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0382
  time to fit residues: 4.1452
Evaluate side-chains
  57 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0170
   chunk 6 optimal weight:    0.0770
   chunk 38 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 ASN
B 548 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.080603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.067544 restraints weight = 31518.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.069372 restraints weight = 21638.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070713 restraints weight = 16215.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.071774 restraints weight = 12873.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.072568 restraints weight = 10657.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5530  Z= 0.093
  Angle     :  0.561   8.972   7523  Z= 0.275
  Chirality :  0.044   0.264    862
  Planarity :  0.004   0.050    939
  Dihedral  : 13.092 179.556    816
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.31 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.32), residues: 649
  helix:  0.24 (0.38), residues: 201
  sheet: -0.20 (0.46), residues: 122
  loop : -1.43 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.013   0.001   TYR B 635 
 PHE   0.015   0.001   PHE B 217 
 TRP   0.005   0.001   TRP B 618 
 HIS   0.002   0.000   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 5530)
  covalent geometry    : angle       0.56130 ( 7523)
  hydrogen bonds       : bond        0.02777 (  182)
  hydrogen bonds       : angle       5.37767 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8570 (p0) cc_final: 0.8247 (p0)
REVERT: B  269 ASP cc_start: 0.8731 (t0) cc_final: 0.8025 (t0)
REVERT: B  416 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: B  419 GLN cc_start: 0.9313 (pp30) cc_final: 0.9074 (pp30)
REVERT: B  507 GLU cc_start: 0.9245 (mp0) cc_final: 0.8787 (pm20)
REVERT: B  525 ILE cc_start: 0.9109 (tt) cc_final: 0.8857 (mm)
REVERT: B  599 MET cc_start: 0.9010 (tmm) cc_final: 0.8633 (tmm)
REVERT: B  628 MET cc_start: 0.7325 (tpt) cc_final: 0.7018 (tpt)
REVERT: B  746 ASN cc_start: 0.8721 (p0) cc_final: 0.8260 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0584
  time to fit residues: 6.4454
Evaluate side-chains
  61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 64 optimal weight:    0.6980
   chunk 9 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0970
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    0.2980
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.9980

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 ASN
B 548 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.080340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.067201 restraints weight = 30768.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.068992 restraints weight = 21365.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.070320 restraints weight = 16094.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.071345 restraints weight = 12857.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.072123 restraints weight = 10687.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5530  Z= 0.100
  Angle     :  0.560   8.608   7523  Z= 0.275
  Chirality :  0.043   0.262    862
  Planarity :  0.004   0.048    939
  Dihedral  : 12.959 179.258    816
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.93 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.32), residues: 649
  helix:  0.21 (0.38), residues: 201
  sheet: -0.17 (0.47), residues: 122
  loop : -1.36 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 174 
 TYR   0.008   0.001   TYR B 861 
 PHE   0.013   0.002   PHE B 217 
 TRP   0.005   0.001   TRP B 618 
 HIS   0.002   0.000   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5530)
  covalent geometry    : angle       0.56015 ( 7523)
  hydrogen bonds       : bond        0.02796 (  182)
  hydrogen bonds       : angle       5.29593 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  244 ASN cc_start: 0.8635 (p0) cc_final: 0.8375 (p0)
REVERT: B  269 ASP cc_start: 0.8729 (t0) cc_final: 0.8020 (t0)
REVERT: B  419 GLN cc_start: 0.9326 (pp30) cc_final: 0.9094 (pp30)
REVERT: B  476 PHE cc_start: 0.8961 (m-80) cc_final: 0.8677 (m-10)
REVERT: B  507 GLU cc_start: 0.9269 (mp0) cc_final: 0.8796 (pm20)
REVERT: B  599 MET cc_start: 0.9049 (tmm) cc_final: 0.8682 (tmm)
REVERT: B  628 MET cc_start: 0.7341 (tpt) cc_final: 0.7036 (tpt)
REVERT: B  746 ASN cc_start: 0.8714 (p0) cc_final: 0.8273 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0446
  time to fit residues: 4.7948
Evaluate side-chains
  60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0770
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0370
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.081500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.068429 restraints weight = 30315.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.070279 restraints weight = 20721.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.071620 restraints weight = 15488.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.072666 restraints weight = 12286.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.073465 restraints weight = 10170.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5530  Z= 0.094
  Angle     :  0.582   8.297   7523  Z= 0.284
  Chirality :  0.044   0.279    862
  Planarity :  0.004   0.049    939
  Dihedral  : 12.742 179.600    816
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.47 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.32), residues: 649
  helix:  0.09 (0.38), residues: 201
  sheet: -0.20 (0.47), residues: 128
  loop : -1.35 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.008   0.001   TYR B 575 
 PHE   0.012   0.002   PHE B 476 
 TRP   0.004   0.001   TRP B 618 
 HIS   0.002   0.000   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 5530)
  covalent geometry    : angle       0.58232 ( 7523)
  hydrogen bonds       : bond        0.02627 (  182)
  hydrogen bonds       : angle       5.15138 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B  244 ASN cc_start: 0.8657 (p0) cc_final: 0.8383 (p0)
REVERT: B  269 ASP cc_start: 0.8697 (t0) cc_final: 0.8025 (t0)
REVERT: B  419 GLN cc_start: 0.9322 (pp30) cc_final: 0.9100 (pp30)
REVERT: B  507 GLU cc_start: 0.9260 (mp0) cc_final: 0.8764 (pm20)
REVERT: B  525 ILE cc_start: 0.7767 (mm) cc_final: 0.7452 (tt)
REVERT: B  599 MET cc_start: 0.9017 (tmm) cc_final: 0.8649 (tmm)
REVERT: B  628 MET cc_start: 0.7264 (tpt) cc_final: 0.6932 (tpt)
REVERT: B  746 ASN cc_start: 0.8718 (p0) cc_final: 0.8278 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0376
  time to fit residues: 4.2692
Evaluate side-chains
  60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0870
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.080962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068078 restraints weight = 30937.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069899 restraints weight = 21190.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.071291 restraints weight = 15841.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.072345 restraints weight = 12500.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.073149 restraints weight = 10311.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5530  Z= 0.095
  Angle     :  0.585   8.185   7523  Z= 0.283
  Chirality :  0.044   0.310    862
  Planarity :  0.004   0.049    939
  Dihedral  : 12.573 179.398    816
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.31 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.32), residues: 649
  helix:  0.12 (0.38), residues: 201
  sheet: -0.20 (0.47), residues: 128
  loop : -1.35 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 756 
 TYR   0.007   0.001   TYR B 506 
 PHE   0.011   0.002   PHE B 253 
 TRP   0.003   0.001   TRP B 479 
 HIS   0.002   0.000   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 5530)
  covalent geometry    : angle       0.58468 ( 7523)
  hydrogen bonds       : bond        0.02688 (  182)
  hydrogen bonds       : angle       5.01674 (  507)

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: B  269 ASP cc_start: 0.8844 (t0) cc_final: 0.8268 (t0)
REVERT: B  286 ASN cc_start: 0.8930 (m110) cc_final: 0.8708 (t0)
REVERT: B  414 THR cc_start: 0.9798 (p) cc_final: 0.9594 (p)
REVERT: B  419 GLN cc_start: 0.9333 (pp30) cc_final: 0.9123 (pp30)
REVERT: B  476 PHE cc_start: 0.8933 (m-80) cc_final: 0.8668 (m-10)
REVERT: B  507 GLU cc_start: 0.9242 (mp0) cc_final: 0.8777 (pm20)
REVERT: B  525 ILE cc_start: 0.7769 (mm) cc_final: 0.7468 (tt)
REVERT: B  599 MET cc_start: 0.9169 (tmm) cc_final: 0.8805 (tmm)
REVERT: B  628 MET cc_start: 0.7276 (tpt) cc_final: 0.6937 (tpt)
REVERT: B  746 ASN cc_start: 0.8705 (p0) cc_final: 0.8266 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0451
  time to fit residues: 4.4097
Evaluate side-chains
  60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0010
   chunk 64 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0060
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0270
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.7862

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.080729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068003 restraints weight = 31557.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069872 restraints weight = 21614.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.071232 restraints weight = 16069.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.072270 restraints weight = 12673.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.073059 restraints weight = 10463.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5530  Z= 0.093
  Angle     :  0.568   7.997   7523  Z= 0.277
  Chirality :  0.043   0.301    862
  Planarity :  0.004   0.049    939
  Dihedral  : 12.372 179.072    816
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.16 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.32), residues: 649
  helix:  0.20 (0.38), residues: 200
  sheet: -0.14 (0.47), residues: 124
  loop : -1.37 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.007   0.001   TYR B 234 
 PHE   0.012   0.001   PHE B 253 
 TRP   0.004   0.001   TRP B 479 
 HIS   0.003   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 5530)
  covalent geometry    : angle       0.56839 ( 7523)
  hydrogen bonds       : bond        0.02638 (  182)
  hydrogen bonds       : angle       5.03366 (  507)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 871.05 seconds
wall clock time: 15 minutes 53.06 seconds (953.06 seconds total)