Starting phenix.real_space_refine
on Tue Aug  4 17:41:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9shq_54908/08_2026/9shq_54908.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9shq_54908/08_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_54908/08_2026/9shq_54908.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9shq_54908/08_2026/9shq_54908.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9shq_54908/08_2026/9shq_54908.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9shq_54908/08_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 1.04, per 1000 atoms: 0.19
  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: 0.29
  Conformation dependent library (CDL) restraints added in 180.2 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: 0.16
  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: 0.63

  Time building geometry restraints manager: 0.44 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=" P     U D   2 "
       pdb=" O5'   U D   2 "
    ideal  model  delta    sigma   weight residual
    1.593  1.617 -0.024 1.00e-02 1.00e+04 5.59e+00
  bond pdb=" P     A C   3 "
       pdb=" O5'   A C   3 "
    ideal  model  delta    sigma   weight residual
    1.593  1.617 -0.024 1.00e-02 1.00e+04 5.53e+00
  bond pdb=" P     U C   2 "
       pdb=" O5'   U C   2 "
    ideal  model  delta    sigma   weight residual
    1.593  1.616 -0.023 1.00e-02 1.00e+04 5.22e+00
  bond pdb=" P     C D   3 "
       pdb=" O5'   C D   3 "
    ideal  model  delta    sigma   weight residual
    1.593  1.614 -0.021 1.00e-02 1.00e+04 4.62e+00
  bond pdb=" P     U C   1 "
       pdb=" O5'   U C   1 "
    ideal  model  delta    sigma   weight residual
    1.593  1.614 -0.021 1.00e-02 1.00e+04 4.35e+00
  ... (remaining 5525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 7412
        2.52 -     5.03: 94
        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=" O4'   C D   3 "
        pdb=" C4'   C D   3 "
        pdb=" C3'   C D   3 "
      ideal   model   delta    sigma   weight residual
     106.10  103.50    2.60 8.00e-01 1.56e+00 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=" C3'   U C   2 "
        pdb=" O3'   U C   2 "
        pdb=" P     A C   3 "
      ideal   model   delta    sigma   weight residual
     119.70  123.12   -3.42 1.20e+00 6.94e-01 8.10e+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: 836
       0.115 -    0.230: 19
       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:             0.110
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.290
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
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= 0.189
  Angle     :  0.715  12.584   7523  Z= 0.364
  Chirality :  0.062   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/Z
  covalent geometry    : bond        0.00339 /  0.19 ( 5530)
  covalent geometry    : angle       0.71509 /  0.36 ( 7523)
  hydrogen bonds       : bond        0.30401 / 19.12 (  182)
  hydrogen bonds       : angle       9.44578 /  6.55 (  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  : 0.147 
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: 0.0425
  time to fit residues: 5.0342
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  : 0.132 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 177 HIS
B 610 ASN
B 810 GLN
B 822 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.080894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.067471 restraints weight = 31012.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.069342 restraints weight = 21496.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.070741 restraints weight = 16145.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.071810 restraints weight = 12850.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.072634 restraints weight = 10660.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5530  Z= 0.144
  Angle     :  0.614  11.205   7523  Z= 0.318
  Chirality :  0.045   0.153    862
  Planarity :  0.005   0.076    939
  Dihedral  : 13.545 179.790    816
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.30), residues: 649
  helix: -0.48 (0.35), residues: 199
  sheet: -0.00 (0.47), residues: 115
  loop : -1.70 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 538 
 TYR   0.013   0.002   TYR B 575 
 PHE   0.018   0.002   PHE B 253 
 TRP   0.008   0.001   TRP B 250 
 HIS   0.006   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 5530)
  covalent geometry    : angle       0.61450 /  0.32 ( 7523)
  hydrogen bonds       : bond        0.05754 /  3.61 (  182)
  hydrogen bonds       : angle       7.10681 /  4.96 (  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
  75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  414 THR cc_start: 0.9528 (p) cc_final: 0.9123 (t)
REVERT: B  417 GLN cc_start: 0.8900 (mt0) cc_final: 0.8339 (mt0)
REVERT: B  499 LEU cc_start: 0.9322 (tp) cc_final: 0.8829 (mp)
REVERT: B  599 MET cc_start: 0.9202 (tmm) cc_final: 0.8938 (tmm)
REVERT: B  633 ASP cc_start: 0.8774 (t70) cc_final: 0.8519 (t70)
REVERT: B  703 ASP cc_start: 0.8317 (t70) cc_final: 0.7644 (t70)
REVERT: B  746 ASN cc_start: 0.8521 (p0) cc_final: 0.8057 (p0)
REVERT: B  782 SER cc_start: 0.9426 (p) cc_final: 0.9145 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0396
  time to fit residues: 4.2506
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    0.0020
   chunk 55 optimal weight:    0.2980
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.4192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 232 ASN
B 810 GLN
B 822 ASN
** 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 = 0.3686 r_free = 0.3686 target = 0.080803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.067682 restraints weight = 30646.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.069577 restraints weight = 20970.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.070999 restraints weight = 15623.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.072056 restraints weight = 12342.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.072870 restraints weight = 10166.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.1898

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= 0.125
  Angle     :  0.551  10.154   7523  Z= 0.284
  Chirality :  0.044   0.189    862
  Planarity :  0.004   0.063    939
  Dihedral  : 13.490 179.490    816
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  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: -0.27 (0.36), residues: 200
  sheet:  0.01 (0.47), residues: 117
  loop : -1.68 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 398 
 TYR   0.010   0.001   TYR B 575 
 PHE   0.015   0.002   PHE B 517 
 TRP   0.007   0.001   TRP B 479 
 HIS   0.005   0.001   HIS B 794 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 5530)
  covalent geometry    : angle       0.55095 /  0.28 ( 7523)
  hydrogen bonds       : bond        0.04916 /  3.11 (  182)
  hydrogen bonds       : angle       6.61991 /  4.64 (  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
  75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 THR cc_start: 0.8290 (p) cc_final: 0.8022 (p)
REVERT: B  264 ILE cc_start: 0.9021 (tt) cc_final: 0.8736 (mp)
REVERT: B  499 LEU cc_start: 0.9389 (tp) cc_final: 0.8949 (mp)
REVERT: B  527 MET cc_start: 0.7451 (pmm) cc_final: 0.7003 (pmm)
REVERT: B  599 MET cc_start: 0.9189 (tmm) cc_final: 0.8896 (tmm)
REVERT: B  746 ASN cc_start: 0.8549 (p0) cc_final: 0.8085 (p0)
REVERT: B  782 SER cc_start: 0.9391 (p) cc_final: 0.9148 (t)
REVERT: B  833 CYS cc_start: 0.9118 (m) cc_final: 0.8733 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0466
  time to fit residues: 4.9702
Evaluate side-chains
  58 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 57 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    3.4086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 515 ASN
B 548 GLN
** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 822 ASN
** 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 = 0.3605 r_free = 0.3605 target = 0.077315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.064106 restraints weight = 31730.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.065800 restraints weight = 22214.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.067115 restraints weight = 16965.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068104 restraints weight = 13636.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.068869 restraints weight = 11443.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5530  Z= 0.218
  Angle     :  0.663   9.688   7523  Z= 0.352
  Chirality :  0.045   0.150    862
  Planarity :  0.005   0.056    939
  Dihedral  : 13.711 177.379    816
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.37 %
    Favored  : 93.46 %
  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: -1.47 (0.31), residues: 649
  helix: -0.19 (0.37), residues: 198
  sheet: -0.47 (0.46), residues: 115
  loop : -1.65 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 538 
 TYR   0.015   0.002   TYR B 313 
 PHE   0.019   0.003   PHE B 253 
 TRP   0.012   0.002   TRP B 823 
 HIS   0.010   0.002   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.22 ( 5530)
  covalent geometry    : angle       0.66339 /  0.35 ( 7523)
  hydrogen bonds       : bond        0.04432 /  2.81 (  182)
  hydrogen bonds       : angle       6.53580 /  4.55 (  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
  72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8509 (p0) cc_final: 0.8293 (p0)
REVERT: B  254 THR cc_start: 0.8256 (p) cc_final: 0.7962 (p)
REVERT: B  275 LEU cc_start: 0.9404 (tt) cc_final: 0.9181 (mp)
REVERT: B  599 MET cc_start: 0.9039 (tmm) cc_final: 0.8696 (tmm)
REVERT: B  633 ASP cc_start: 0.9065 (t70) cc_final: 0.6661 (t70)
REVERT: B  746 ASN cc_start: 0.8644 (p0) cc_final: 0.8162 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 72
  average time/residue: 0.0491
  time to fit residues: 4.8709
Evaluate side-chains
  60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 286 ASN
B 548 GLN
B 585 GLN
B 759 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 = 0.3661 r_free = 0.3661 target = 0.079982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.066702 restraints weight = 31379.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068519 restraints weight = 21636.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.069898 restraints weight = 16282.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.070937 restraints weight = 12951.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.071773 restraints weight = 10758.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5530  Z= 0.110
  Angle     :  0.593  11.110   7523  Z= 0.296
  Chirality :  0.045   0.181    862
  Planarity :  0.004   0.052    939
  Dihedral  : 13.478 178.881    816
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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: -1.32 (0.32), residues: 649
  helix: -0.01 (0.38), residues: 200
  sheet: -0.28 (0.46), residues: 121
  loop : -1.67 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 418 
 TYR   0.012   0.001   TYR B 861 
 PHE   0.021   0.002   PHE B 170 
 TRP   0.006   0.001   TRP B 618 
 HIS   0.004   0.001   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 5530)
  covalent geometry    : angle       0.59310 /  0.30 ( 7523)
  hydrogen bonds       : bond        0.03643 /  2.34 (  182)
  hydrogen bonds       : angle       6.12979 /  4.28 (  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
  72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8524 (p0) cc_final: 0.8288 (p0)
REVERT: B  254 THR cc_start: 0.8316 (p) cc_final: 0.8005 (p)
REVERT: B  527 MET cc_start: 0.7917 (pmm) cc_final: 0.7449 (pmm)
REVERT: B  599 MET cc_start: 0.9022 (tmm) cc_final: 0.8672 (tmm)
REVERT: B  746 ASN cc_start: 0.8603 (p0) cc_final: 0.8115 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0515
  time to fit residues: 5.3400
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  : 0.239 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 24 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3648 r_free = 0.3648 target = 0.079274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066090 restraints weight = 31266.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.067844 restraints weight = 21833.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.069166 restraints weight = 16565.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.070155 restraints weight = 13291.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.070940 restraints weight = 11117.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3213

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= 0.125
  Angle     :  0.571   9.865   7523  Z= 0.288
  Chirality :  0.043   0.182    862
  Planarity :  0.004   0.051    939
  Dihedral  : 13.410 178.804    816
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.31 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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: -1.29 (0.32), residues: 649
  helix:  0.06 (0.38), residues: 200
  sheet: -0.35 (0.47), residues: 115
  loop : -1.63 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 662 
 TYR   0.012   0.001   TYR B 428 
 PHE   0.017   0.002   PHE B 170 
 TRP   0.006   0.001   TRP B 618 
 HIS   0.006   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 5530)
  covalent geometry    : angle       0.57076 /  0.29 ( 7523)
  hydrogen bonds       : bond        0.03428 /  2.15 (  182)
  hydrogen bonds       : angle       5.91509 /  4.13 (  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
  66 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8549 (p0) cc_final: 0.8301 (p0)
REVERT: B  254 THR cc_start: 0.8382 (p) cc_final: 0.8106 (p)
REVERT: B  599 MET cc_start: 0.9013 (tmm) cc_final: 0.8657 (tmm)
REVERT: B  746 ASN cc_start: 0.8604 (p0) cc_final: 0.8126 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0475
  time to fit residues: 4.4706
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  : 0.121 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3665 r_free = 0.3665 target = 0.079864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.066713 restraints weight = 31067.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.068530 restraints weight = 21256.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069878 restraints weight = 15878.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.070906 restraints weight = 12606.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.071704 restraints weight = 10452.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5530  Z= 0.107
  Angle     :  0.582   9.283   7523  Z= 0.287
  Chirality :  0.044   0.181    862
  Planarity :  0.004   0.048    939
  Dihedral  : 13.287 179.250    816
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.16 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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: -1.25 (0.32), residues: 649
  helix: -0.00 (0.38), residues: 201
  sheet: -0.31 (0.46), residues: 120
  loop : -1.56 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 420 
 TYR   0.011   0.001   TYR B 861 
 PHE   0.020   0.002   PHE B 170 
 TRP   0.008   0.001   TRP B 250 
 HIS   0.002   0.000   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 ( 5530)
  covalent geometry    : angle       0.58249 /  0.29 ( 7523)
  hydrogen bonds       : bond        0.03264 /  2.09 (  182)
  hydrogen bonds       : angle       5.71890 /  3.97 (  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
  69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8527 (p0) cc_final: 0.8211 (p0)
REVERT: B  416 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7879 (mm-30)
REVERT: B  599 MET cc_start: 0.8988 (tmm) cc_final: 0.8614 (tmm)
REVERT: B  680 LEU cc_start: 0.9783 (tp) cc_final: 0.9581 (tt)
REVERT: B  746 ASN cc_start: 0.8576 (p0) cc_final: 0.8208 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0527
  time to fit residues: 5.2570
Evaluate side-chains
  58 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    2.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 548 GLN
** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 822 ASN
** 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 = 0.3615 r_free = 0.3615 target = 0.077129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.064259 restraints weight = 31653.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.065960 restraints weight = 21990.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067259 restraints weight = 16656.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068218 restraints weight = 13319.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.068972 restraints weight = 11133.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5530  Z= 0.180
  Angle     :  0.622   8.809   7523  Z= 0.317
  Chirality :  0.045   0.194    862
  Planarity :  0.004   0.044    939
  Dihedral  : 13.315 178.471    816
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.24 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  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: -1.39 (0.32), residues: 649
  helix: -0.14 (0.36), residues: 201
  sheet: -0.42 (0.48), residues: 115
  loop : -1.61 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 276 
 TYR   0.015   0.002   TYR B 542 
 PHE   0.014   0.002   PHE B 253 
 TRP   0.014   0.002   TRP B 823 
 HIS   0.008   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.18 ( 5530)
  covalent geometry    : angle       0.62162 /  0.32 ( 7523)
  hydrogen bonds       : bond        0.03572 /  2.27 (  182)
  hydrogen bonds       : angle       5.85698 /  4.06 (  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
  68 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8578 (p0) cc_final: 0.8315 (p0)
REVERT: B  599 MET cc_start: 0.9018 (tmm) cc_final: 0.8664 (tmm)
REVERT: B  746 ASN cc_start: 0.8584 (p0) cc_final: 0.8257 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0580
  time to fit residues: 5.6213
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  : 0.203 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0970
   chunk 59 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 286 ASN
B 548 GLN
B 834 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 = 0.3644 r_free = 0.3644 target = 0.078684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.065425 restraints weight = 30875.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.067131 restraints weight = 21658.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.068431 restraints weight = 16564.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.069418 restraints weight = 13362.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.070149 restraints weight = 11219.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5530  Z= 0.116
  Angle     :  0.600   8.284   7523  Z= 0.295
  Chirality :  0.044   0.200    862
  Planarity :  0.004   0.046    939
  Dihedral  : 13.125 179.608    816
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.16 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -1.35 (0.32), residues: 649
  helix: -0.13 (0.37), residues: 201
  sheet: -0.51 (0.47), residues: 115
  loop : -1.51 (0.32), residues: 333

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   0.017   0.002   PHE B 253 
 TRP   0.007   0.001   TRP B 823 
 HIS   0.003   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 5530)
  covalent geometry    : angle       0.60037 /  0.30 ( 7523)
  hydrogen bonds       : bond        0.03189 /  2.05 (  182)
  hydrogen bonds       : angle       5.67540 /  3.94 (  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
  71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8585 (p0) cc_final: 0.8320 (p0)
REVERT: B  525 ILE cc_start: 0.9089 (tt) cc_final: 0.8888 (mm)
REVERT: B  599 MET cc_start: 0.9000 (tmm) cc_final: 0.8626 (tmm)
REVERT: B  746 ASN cc_start: 0.8573 (p0) cc_final: 0.8205 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0398
  time to fit residues: 4.0418
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  : 0.217 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 8 optimal weight:    0.4980
   chunk 2 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0050
   chunk 36 optimal weight:    0.0010
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.6602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3665 r_free = 0.3665 target = 0.079750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.066487 restraints weight = 31183.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.068235 restraints weight = 21801.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.069531 restraints weight = 16586.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070516 restraints weight = 13348.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.071302 restraints weight = 11191.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5530  Z= 0.098
  Angle     :  0.594   8.168   7523  Z= 0.288
  Chirality :  0.044   0.244    862
  Planarity :  0.004   0.047    939
  Dihedral  : 12.925 179.847    816
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 11.16
  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: -1.36 (0.32), residues: 649
  helix: -0.11 (0.38), residues: 201
  sheet: -0.61 (0.47), residues: 117
  loop : -1.50 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 276 
 TYR   0.012   0.001   TYR B 575 
 PHE   0.013   0.002   PHE B 170 
 TRP   0.008   0.001   TRP B 618 
 HIS   0.002   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.10 ( 5530)
  covalent geometry    : angle       0.59370 /  0.29 ( 7523)
  hydrogen bonds       : bond        0.03023 /  1.94 (  182)
  hydrogen bonds       : angle       5.47225 /  3.81 (  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
  69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ASN cc_start: 0.8615 (p0) cc_final: 0.8337 (p0)
REVERT: B  507 GLU cc_start: 0.9250 (mp0) cc_final: 0.8724 (pm20)
REVERT: B  525 ILE cc_start: 0.9076 (tt) cc_final: 0.8870 (mm)
REVERT: B  599 MET cc_start: 0.8996 (tmm) cc_final: 0.8623 (tmm)
REVERT: B  622 MET cc_start: 0.5304 (mtt) cc_final: 0.5080 (mtt)
REVERT: B  746 ASN cc_start: 0.8558 (p0) cc_final: 0.8183 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0518
  time to fit residues: 5.1050
Evaluate side-chains
  58 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 50 optimal weight:    0.2980
   chunk 20 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 286 ASN
B 510 ASN
** 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 = 0.079937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.066790 restraints weight = 30941.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.068577 restraints weight = 21488.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069876 restraints weight = 16239.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.070875 restraints weight = 13025.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.071648 restraints weight = 10860.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5530  Z= 0.097
  Angle     :  0.589   8.145   7523  Z= 0.284
  Chirality :  0.044   0.237    862
  Planarity :  0.004   0.046    939
  Dihedral  : 12.760 179.645    816
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.31 %
    Favored  : 97.53 %
  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: -1.33 (0.32), residues: 649
  helix: -0.15 (0.37), residues: 201
  sheet: -0.59 (0.47), residues: 117
  loop : -1.44 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 420 
 TYR   0.007   0.001   TYR B 234 
 PHE   0.014   0.002   PHE B 170 
 TRP   0.007   0.001   TRP B 618 
 HIS   0.002   0.001   HIS B 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 5530)
  covalent geometry    : angle       0.58856 /  0.28 ( 7523)
  hydrogen bonds       : bond        0.02925 /  1.88 (  182)
  hydrogen bonds       : angle       5.36876 /  3.73 (  507)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 794.48 seconds
wall clock time: 14 minutes 21.25 seconds (861.25 seconds total)