Starting phenix.real_space_refine
on Thu Jul  2 02:43:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s0z_54428/07_2026/9s0z_54428.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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       5      5.49       5
     Mg      1      5.21       5
     S      32      5.16       5
     C    3680      2.51       5
     N    1014      2.21       5
     O    1063      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5795
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 5691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 704, 5691
          Classifications: {'peptide': 704}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 671}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 103
          Classifications: {'RNA': 5}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 1, 'rna3p': 3}
    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: 1.59, per 1000 atoms: 0.27
  Number of scatterers: 5795
  At special positions: 0
  Unit cell: (79.056, 92.232, 111.264, 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      32     16.00
     P       5     15.00
     Mg      1     11.99
     O    1063      8.00
     N    1014      7.00
     C    3680      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: 0.53
  Conformation dependent library (CDL) restraints added in 438.5 milliseconds
  

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      34.9% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 154 through 159
    Processing helix  chain 'B' and resid 206 through 223
    Processing helix  chain 'B' and resid 279 through 289
    Processing helix  chain 'B' and resid 299 through 306
      removed outlier: 4.039A  pdb=" N   GLY B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 350
    Processing helix  chain 'B' and resid 400 through 407
    Processing helix  chain 'B' and resid 407 through 412
    Processing helix  chain 'B' and resid 414 through 432
      removed outlier: 4.021A  pdb=" N   LEU B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 443
    Processing helix  chain 'B' and resid 505 through 524
      removed outlier: 3.509A  pdb=" N   ILE B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
      Proline residue:  B 521  - end of helix
    Processing helix  chain 'B' and resid 538 through 550
      removed outlier: 3.529A  pdb=" N   GLN B 548 " --> pdb=" O   ARG B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 579
      removed outlier: 3.683A  pdb=" N   TYR B 569 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 597 through 614
      removed outlier: 3.713A  pdb=" N   GLY B 614 " --> pdb=" O   ASN B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 673 through 691
      removed outlier: 3.666A  pdb=" N   GLN B 681 " --> pdb=" O   LYS B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 716
      removed outlier: 3.795A  pdb=" N   LEU B 713 " --> pdb=" O   GLN B 709 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 714 " --> pdb=" O   LEU B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 727
      removed outlier: 3.532A  pdb=" N   ASP B 723 " --> pdb=" O   PRO B 719 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 805 through 816
    Processing helix  chain 'B' and resid 817 through 819
      No H-bonds generated for 'chain 'B' and resid 817 through 819'
    Processing helix  chain 'B' and resid 830 through 846
    Processing helix  chain 'B' and resid 852 through 856
      removed outlier: 3.691A  pdb=" N   LEU B 855 " --> pdb=" O   ASN B 852 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 659 through 664
      removed outlier: 3.669A  pdb=" N   ASP B 633 " --> pdb=" O   GLY B 647 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ILE B 629 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   CYS B 634 " --> pdb=" O   ASP B 703 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL B 698 " --> pdb=" O   THR B 737 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ILE B 739 " --> pdb=" O   VAL B 698 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL B 700 " --> pdb=" O   ILE B 739 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   VAL B 741 " --> pdb=" O   VAL B 700 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ARG B 702 " --> pdb=" O   VAL B 741 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU B 736 " --> pdb=" O   ASP B 800 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ASP B 800 " --> pdb=" O   LEU B 736 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 798 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LYS B 114 " --> pdb=" O   GLN B 752 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLN B 752 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 257 through 259
      removed outlier: 5.224A  pdb=" N   ILE B 264 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138
      removed outlier: 5.524A  pdb=" N   LEU B 198 " --> pdb=" O   HIS B 134 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   HIS B 134 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN B 200 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 138
    Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229
    Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 242
    Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 319
      removed outlier: 3.596A  pdb=" N   VAL B 309 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ILE B 308 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464
      removed outlier: 3.628A  pdb=" N   ILE B 463 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 531 through 535
      removed outlier: 6.283A  pdb=" N   LEU B 499 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL B 535 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   TYR B 501 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   THR B 502 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   VAL B 557 " --> pdb=" O   GLN B 585 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   VAL B 587 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   CYS B 559 " --> pdb=" O   VAL B 587 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    678 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: 1.03

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1672
        1.33 -     1.45: 926
        1.45 -     1.57: 3273
        1.57 -     1.69: 9
        1.69 -     1.81: 48
  Bond restraints: 5928
  Sorted by residual:
  bond pdb=" O5'   A C   3 "
       pdb=" C5'   A C   3 "
    ideal  model  delta    sigma   weight residual
    1.420  1.453 -0.033 1.50e-02 4.44e+03 4.95e+00
  bond pdb=" P     A C   3 "
       pdb=" OP2   A C   3 "
    ideal  model  delta    sigma   weight residual
    1.485  1.517 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" P     A C   3 "
       pdb=" O5'   A C   3 "
    ideal  model  delta    sigma   weight residual
    1.593  1.615 -0.022 1.50e-02 4.44e+03 2.16e+00
  bond pdb=" CG1 ILE B 827 "
       pdb=" CD1 ILE B 827 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.42e+00
  bond pdb=" C1'   A C   3 "
       pdb=" N9    A C   3 "
    ideal  model  delta    sigma   weight residual
    1.475  1.457  0.018 1.50e-02 4.44e+03 1.37e+00
  ... (remaining 5923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 7845
        1.59 -     3.19: 176
        3.19 -     4.78: 27
        4.78 -     6.38: 5
        6.38 -     7.97: 5
  Bond angle restraints: 8058
  Sorted by residual:
  angle pdb=" C   SER B 237 "
        pdb=" N   ASP B 238 "
        pdb=" CA  ASP B 238 "
      ideal   model   delta    sigma   weight residual
     123.46  119.93    3.53 1.35e+00 5.49e-01 6.82e+00
  angle pdb=" O2'   A C   3 "
        pdb=" C2'   A C   3 "
        pdb=" C1'   A C   3 "
      ideal   model   delta    sigma   weight residual
     108.40  112.01   -3.61 1.50e+00 4.44e-01 5.81e+00
  angle pdb=" O3'   U C   2 "
        pdb=" P     A C   3 "
        pdb=" OP2   A C   3 "
      ideal   model   delta    sigma   weight residual
     108.00  115.19   -7.19 3.00e+00 1.11e-01 5.75e+00
  angle pdb=" CA  LEU B 363 "
        pdb=" CB  LEU B 363 "
        pdb=" CG  LEU B 363 "
      ideal   model   delta    sigma   weight residual
     116.30  124.27   -7.97 3.50e+00 8.16e-02 5.18e+00
  angle pdb=" C   ILE B 384 "
        pdb=" CA  ILE B 384 "
        pdb=" CB  ILE B 384 "
      ideal   model   delta    sigma   weight residual
     110.89  113.20   -2.31 1.08e+00 8.57e-01 4.59e+00
  ... (remaining 8053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.42: 3227
       18.42 -    36.83: 282
       36.83 -    55.25: 49
       55.25 -    73.67: 9
       73.67 -    92.08: 12
  Dihedral angle restraints: 3579
    sinusoidal: 1510
      harmonic: 2069
  Sorted by residual:
  dihedral pdb=" CA  ASP B 433 "
           pdb=" CB  ASP B 433 "
           pdb=" CG  ASP B 433 "
           pdb=" OD1 ASP B 433 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.05   56.05     1      2.00e+01 2.50e-03 1.06e+01
  dihedral pdb=" CA  GLU B 654 "
           pdb=" C   GLU B 654 "
           pdb=" N   GLY B 655 "
           pdb=" CA  GLY B 655 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.30  -15.70     0      5.00e+00 4.00e-02 9.86e+00
  dihedral pdb=" CA  GLN B 720 "
           pdb=" C   GLN B 720 "
           pdb=" N   PHE B 721 "
           pdb=" CA  PHE B 721 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.68   15.32     0      5.00e+00 4.00e-02 9.39e+00
  ... (remaining 3576 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 821
       0.080 -    0.161: 85
       0.161 -    0.241: 1
       0.241 -    0.322: 1
       0.322 -    0.402: 1
  Chirality restraints: 909
  Sorted by residual:
  chirality pdb=" P     A C   3 "
            pdb=" OP1   A C   3 "
            pdb=" OP2   A C   3 "
            pdb=" O5'   A C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.81   -0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CB  ILE B 457 "
            pdb=" CA  ILE B 457 "
            pdb=" CG1 ILE B 457 "
            pdb=" CG2 ILE B 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" C2'   A C   3 "
            pdb=" C3'   A C   3 "
            pdb=" O2'   A C   3 "
            pdb=" C1'   A C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.54   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 906 not shown)

  Planarity restraints: 1009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 497 "   -0.007 2.00e-02 2.50e+03   9.19e-03 2.11e+00
        pdb=" CG  TRP B 497 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 497 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 497 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 497 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 497 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 497 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 497 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 497 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 497 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 705 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   VAL B 705 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   VAL B 705 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY B 706 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 829 "   -0.022 5.00e-02 4.00e+02   3.27e-02 1.72e+00
        pdb=" N   PRO B 830 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 830 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 830 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1006 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.50: 35
        2.50 -     3.10: 4070
        3.10 -     3.70: 8806
        3.70 -     4.30: 12655
        4.30 -     4.90: 21229
  Nonbonded interactions: 46795
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 608 "
            pdb="MG    MG B 901 "
     model   vdw
     1.895 2.250
  nonbonded pdb=" OP1   U C   1 "
            pdb="MG    MG B 901 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OE1 GLN B 608 "
            pdb="MG    MG B 901 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" OXT LEU B 862 "
            pdb="MG    MG B 901 "
     model   vdw
     2.219 2.170
  nonbonded pdb=" NZ  LYS B 566 "
            pdb=" O   GLN B 845 "
     model   vdw
     2.222 3.120
  ... (remaining 46790 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.130
  Find NCS groups from input model:        0.040
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
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      :  0.005   0.046   5928  Z= 0.208
  Angle     :  0.618   7.969   8058  Z= 0.322
  Chirality :  0.049   0.402    909
  Planarity :  0.004   0.033   1009
  Dihedral  : 15.051  92.082   2243
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.46 (0.31), residues: 692
  helix: -0.72 (0.33), residues: 228
  sheet: -0.81 (0.40), residues: 173
  loop : -1.09 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 772 
 TYR   0.016   0.002   TYR B 313 
 PHE   0.019   0.002   PHE B 470 
 TRP   0.024   0.002   TRP B 497 
 HIS   0.006   0.001   HIS B 245 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00479 /  0.21 ( 5928)
  covalent geometry    : angle       0.61793 /  0.32 ( 8058)
  hydrogen bonds       : bond        0.25702 / 17.81 (  238)
  hydrogen bonds       : angle       9.21969 /  6.36 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B  113 VAL cc_start: 0.7389 (p) cc_final: 0.7020 (t)
REVERT: B  265 MET cc_start: 0.7071 (mtt) cc_final: 0.6779 (mtm)
REVERT: B  476 PHE cc_start: 0.7092 (m-10) cc_final: 0.6768 (m-80)
REVERT: B  494 LEU cc_start: 0.5102 (tp) cc_final: 0.4770 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.5904
  time to fit residues: 79.3130
Evaluate side-chains
  52 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 132 GLN
B 225 ASN
B 475 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.116580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.097198 restraints weight = 14650.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 3.03
r_work: 0.3601 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5928  Z= 0.214
  Angle     :  0.747  10.789   8058  Z= 0.387
  Chirality :  0.051   0.176    909
  Planarity :  0.005   0.047   1009
  Dihedral  :  9.213  95.363    854
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.10 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.17 (0.30), residues: 692
  helix:  0.01 (0.32), residues: 233
  sheet: -0.66 (0.42), residues: 148
  loop : -1.37 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 160 
 TYR   0.016   0.002   TYR B 542 
 PHE   0.017   0.002   PHE B 285 
 TRP   0.020   0.003   TRP B 497 
 HIS   0.005   0.001   HIS B 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.21 ( 5928)
  covalent geometry    : angle       0.74720 /  0.39 ( 8058)
  hydrogen bonds       : bond        0.05286 /  3.73 (  238)
  hydrogen bonds       : angle       6.71192 /  4.66 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B  111 ILE cc_start: 0.7236 (mt) cc_final: 0.7033 (mm)
REVERT: B  176 GLN cc_start: 0.7355 (pm20) cc_final: 0.7136 (pm20)
REVERT: B  220 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (tp)
REVERT: B  224 MET cc_start: 0.8023 (mtp) cc_final: 0.7746 (ptp)
REVERT: B  231 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6413 (mtt-85)
REVERT: B  284 MET cc_start: 0.8217 (mtt) cc_final: 0.7771 (tmm)
REVERT: B  397 MET cc_start: 0.3071 (ptp) cc_final: 0.2613 (ptp)
REVERT: B  476 PHE cc_start: 0.7558 (m-10) cc_final: 0.7258 (m-80)
REVERT: B  532 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.6883 (mmt)
REVERT: B  551 THR cc_start: 0.5782 (p) cc_final: 0.5494 (t)
REVERT: B  628 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7986 (tpp)
  outliers start: 19
  outliers final: 5
  residues processed: 73
  average time/residue: 0.3630
  time to fit residues: 28.3244
Evaluate side-chains
  56 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  231 ARG
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  532 MET
Chi-restraints excluded: chain B residue  628 MET
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 127 GLN
B 510 ASN
B 845 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.112018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.092361 restraints weight = 14297.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.03
r_work: 0.3517 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5928  Z= 0.175
  Angle     :  0.647  12.536   8058  Z= 0.335
  Chirality :  0.047   0.176    909
  Planarity :  0.004   0.047   1009
  Dihedral  :  9.072  93.843    854
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.06 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.04 (0.30), residues: 692
  helix:  0.42 (0.32), residues: 228
  sheet: -1.03 (0.40), residues: 152
  loop : -1.27 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 160 
 TYR   0.013   0.001   TYR B 313 
 PHE   0.012   0.001   PHE B 470 
 TRP   0.008   0.001   TRP B 325 
 HIS   0.004   0.001   HIS B 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.18 ( 5928)
  covalent geometry    : angle       0.64656 /  0.33 ( 8058)
  hydrogen bonds       : bond        0.04486 /  3.17 (  238)
  hydrogen bonds       : angle       5.90877 /  4.09 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 51
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.7733 (mt) cc_final: 0.7517 (mm)
REVERT: B  141 MET cc_start: 0.5458 (mpt) cc_final: 0.5220 (mpt)
REVERT: B  194 ILE cc_start: 0.4354 (mm) cc_final: 0.3995 (mm)
REVERT: B  220 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8092 (tp)
REVERT: B  265 MET cc_start: 0.7933 (mtm) cc_final: 0.7673 (mtm)
REVERT: B  266 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7769 (tm)
REVERT: B  323 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (tp)
REVERT: B  397 MET cc_start: 0.2980 (ptp) cc_final: 0.2537 (ptp)
REVERT: B  476 PHE cc_start: 0.7624 (m-10) cc_final: 0.7358 (m-80)
REVERT: B  551 THR cc_start: 0.6300 (p) cc_final: 0.6064 (t)
REVERT: B  622 MET cc_start: 0.7188 (mmm) cc_final: 0.6770 (mmm)
  outliers start: 24
  outliers final: 9
  residues processed: 65
  average time/residue: 0.3077
  time to fit residues: 21.3678
Evaluate side-chains
  55 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  643 ARG
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 42 optimal weight:    0.0870
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 127 GLN
B 315 ASN
B 845 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.110140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.090326 restraints weight = 14328.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 3.07
r_work: 0.3487 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5928  Z= 0.144
  Angle     :  0.609  13.101   8058  Z= 0.308
  Chirality :  0.046   0.175    909
  Planarity :  0.004   0.044   1009
  Dihedral  :  8.955  92.789    854
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.86 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.07 (0.30), residues: 692
  helix:  0.54 (0.33), residues: 230
  sheet: -1.09 (0.39), residues: 163
  loop : -1.40 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 565 
 TYR   0.023   0.001   TYR B 542 
 PHE   0.023   0.001   PHE B 285 
 TRP   0.025   0.002   TRP B 325 
 HIS   0.003   0.001   HIS B 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 5928)
  covalent geometry    : angle       0.60876 /  0.31 ( 8058)
  hydrogen bonds       : bond        0.03704 /  2.60 (  238)
  hydrogen bonds       : angle       5.52563 /  3.81 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  111 ILE cc_start: 0.7612 (mt) cc_final: 0.7340 (mm)
REVERT: B  141 MET cc_start: 0.5615 (mpt) cc_final: 0.5135 (mpm)
REVERT: B  284 MET cc_start: 0.8311 (mtt) cc_final: 0.7741 (tmm)
REVERT: B  323 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8312 (tp)
REVERT: B  476 PHE cc_start: 0.7722 (m-10) cc_final: 0.7427 (m-80)
REVERT: B  551 THR cc_start: 0.6532 (p) cc_final: 0.6185 (t)
REVERT: B  622 MET cc_start: 0.7628 (mmm) cc_final: 0.7116 (mmm)
REVERT: B  845 GLN cc_start: 0.7906 (tp40) cc_final: 0.7628 (tp-100)
  outliers start: 17
  outliers final: 7
  residues processed: 57
  average time/residue: 0.3449
  time to fit residues: 21.3097
Evaluate side-chains
  47 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 CYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 430 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.104836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084673 restraints weight = 14526.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 3.12
r_work: 0.3375 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5928  Z= 0.210
  Angle     :  0.643  12.753   8058  Z= 0.328
  Chirality :  0.048   0.246    909
  Planarity :  0.005   0.056   1009
  Dihedral  :  8.954  90.295    854
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.81 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.17 (0.31), residues: 692
  helix:  0.48 (0.33), residues: 234
  sheet: -1.32 (0.40), residues: 153
  loop : -1.41 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 643 
 TYR   0.016   0.002   TYR B 693 
 PHE   0.042   0.002   PHE B 665 
 TRP   0.017   0.002   TRP B 325 
 HIS   0.005   0.002   HIS B 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.21 ( 5928)
  covalent geometry    : angle       0.64260 /  0.33 ( 8058)
  hydrogen bonds       : bond        0.04161 /  2.93 (  238)
  hydrogen bonds       : angle       5.52114 /  3.77 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 37
  time to evaluate  : 0.230 
Fit side-chains
REVERT: B  141 MET cc_start: 0.5405 (mpt) cc_final: 0.4709 (mpm)
REVERT: B  266 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7338 (tp)
REVERT: B  323 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8411 (tp)
REVERT: B  476 PHE cc_start: 0.7896 (m-10) cc_final: 0.7667 (m-80)
REVERT: B  785 VAL cc_start: 0.9128 (t) cc_final: 0.8856 (p)
REVERT: B  845 GLN cc_start: 0.8116 (tp40) cc_final: 0.7912 (tp-100)
  outliers start: 22
  outliers final: 7
  residues processed: 55
  average time/residue: 0.3159
  time to fit residues: 18.8178
Evaluate side-chains
  40 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  738 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0870
   chunk 7 optimal weight:    0.1980
   chunk 29 optimal weight:    0.2980
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.2758

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.106901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.086800 restraints weight = 14378.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 3.13
r_work: 0.3417 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5928  Z= 0.112
  Angle     :  0.589  12.279   8058  Z= 0.291
  Chirality :  0.045   0.166    909
  Planarity :  0.004   0.046   1009
  Dihedral  :  8.799  91.686    854
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.03 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 692
  helix:  0.74 (0.33), residues: 235
  sheet: -1.28 (0.40), residues: 148
  loop : -1.33 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 643 
 TYR   0.013   0.001   TYR B 542 
 PHE   0.025   0.001   PHE B 285 
 TRP   0.011   0.001   TRP B 325 
 HIS   0.003   0.001   HIS B 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 5928)
  covalent geometry    : angle       0.58926 /  0.29 ( 8058)
  hydrogen bonds       : bond        0.03410 /  2.40 (  238)
  hydrogen bonds       : angle       5.25915 /  3.59 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7263 (mm)
REVERT: B  141 MET cc_start: 0.5171 (mpt) cc_final: 0.4476 (mpm)
REVERT: B  266 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7875 (tp)
REVERT: B  323 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8300 (tp)
REVERT: B  458 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7613 (mt)
REVERT: B  462 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8336 (mmpt)
REVERT: B  622 MET cc_start: 0.7275 (mmm) cc_final: 0.6615 (mmm)
REVERT: B  845 GLN cc_start: 0.7940 (tp40) cc_final: 0.7716 (tp-100)
  outliers start: 18
  outliers final: 6
  residues processed: 54
  average time/residue: 0.3966
  time to fit residues: 22.8728
Evaluate side-chains
  42 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0670
   chunk 13 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9722

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 399 ASN
** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.106913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.087686 restraints weight = 14404.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.80
r_work: 0.3490 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5928  Z= 0.190
  Angle     :  0.631  12.285   8058  Z= 0.315
  Chirality :  0.046   0.164    909
  Planarity :  0.005   0.049   1009
  Dihedral  :  8.814  89.136    854
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.08 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 692
  helix:  0.65 (0.33), residues: 236
  sheet: -1.26 (0.39), residues: 155
  loop : -1.37 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 643 
 TYR   0.012   0.001   TYR B 542 
 PHE   0.012   0.001   PHE B 470 
 TRP   0.010   0.001   TRP B 687 
 HIS   0.004   0.001   HIS B 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.19 ( 5928)
  covalent geometry    : angle       0.63113 /  0.31 ( 8058)
  hydrogen bonds       : bond        0.03660 /  2.60 (  238)
  hydrogen bonds       : angle       5.34445 /  3.64 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 34
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 MET cc_start: 0.5274 (mpt) cc_final: 0.4989 (mpt)
REVERT: B  266 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (tt)
REVERT: B  323 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (tp)
REVERT: B  622 MET cc_start: 0.7216 (mmm) cc_final: 0.6609 (mmm)
  outliers start: 25
  outliers final: 6
  residues processed: 54
  average time/residue: 0.3830
  time to fit residues: 22.2590
Evaluate side-chains
  39 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 845 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.107633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.088630 restraints weight = 14258.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.81
r_work: 0.3483 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.6221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5928  Z= 0.152
  Angle     :  0.615  12.343   8058  Z= 0.302
  Chirality :  0.045   0.162    909
  Planarity :  0.004   0.043   1009
  Dihedral  :  8.785  89.522    854
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.61 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.97 (0.31), residues: 692
  helix:  0.79 (0.33), residues: 235
  sheet: -1.28 (0.39), residues: 155
  loop : -1.39 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 643 
 TYR   0.012   0.001   TYR B 542 
 PHE   0.027   0.002   PHE B 285 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 794 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 5928)
  covalent geometry    : angle       0.61532 /  0.30 ( 8058)
  hydrogen bonds       : bond        0.03447 /  2.42 (  238)
  hydrogen bonds       : angle       5.26582 /  3.57 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 30
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B  141 MET cc_start: 0.5229 (mpt) cc_final: 0.4945 (mpt)
REVERT: B  266 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (tt)
REVERT: B  284 MET cc_start: 0.7865 (mtt) cc_final: 0.7356 (tmm)
REVERT: B  323 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: B  622 MET cc_start: 0.7280 (mmm) cc_final: 0.6682 (mmm)
REVERT: B  845 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7609 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 41
  average time/residue: 0.3882
  time to fit residues: 17.0322
Evaluate side-chains
  41 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  738 VAL
Chi-restraints excluded: chain B residue  770 VAL
Chi-restraints excluded: chain B residue  845 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 353 GLN
** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.106388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.087077 restraints weight = 14362.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.80
r_work: 0.3466 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.6363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5928  Z= 0.153
  Angle     :  0.618  12.328   8058  Z= 0.304
  Chirality :  0.045   0.164    909
  Planarity :  0.004   0.043   1009
  Dihedral  :  8.774  89.275    854
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 23.45 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 692
  helix:  0.73 (0.33), residues: 235
  sheet: -1.26 (0.40), residues: 155
  loop : -1.41 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 643 
 TYR   0.012   0.001   TYR B 542 
 PHE   0.009   0.001   PHE B 648 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 5928)
  covalent geometry    : angle       0.61804 /  0.30 ( 8058)
  hydrogen bonds       : bond        0.03431 /  2.41 (  238)
  hydrogen bonds       : angle       5.24111 /  3.56 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B  141 MET cc_start: 0.5237 (mpt) cc_final: 0.4953 (mpt)
REVERT: B  266 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: B  622 MET cc_start: 0.7192 (mmm) cc_final: 0.6687 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 40
  average time/residue: 0.3275
  time to fit residues: 14.2988
Evaluate side-chains
  40 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  738 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 59 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 430 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.106042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.086293 restraints weight = 14293.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.86
r_work: 0.3466 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.6609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5928  Z= 0.143
  Angle     :  0.596  12.278   8058  Z= 0.295
  Chirality :  0.045   0.163    909
  Planarity :  0.004   0.041   1009
  Dihedral  :  8.739  89.049    854
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 23.77 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.85 (0.31), residues: 692
  helix:  1.04 (0.33), residues: 229
  sheet: -1.28 (0.40), residues: 158
  loop : -1.35 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 643 
 TYR   0.011   0.001   TYR B 693 
 PHE   0.025   0.002   PHE B 285 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.006   0.001   HIS B 848 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 5928)
  covalent geometry    : angle       0.59589 /  0.29 ( 8058)
  hydrogen bonds       : bond        0.03317 /  2.31 (  238)
  hydrogen bonds       : angle       5.22343 /  3.55 (  678)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.242 
Fit side-chains
REVERT: B  141 MET cc_start: 0.5383 (mpt) cc_final: 0.5121 (mpt)
REVERT: B  284 MET cc_start: 0.7907 (mtt) cc_final: 0.7274 (tmm)
REVERT: B  323 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8348 (tp)
  outliers start: 13
  outliers final: 9
  residues processed: 40
  average time/residue: 0.3296
  time to fit residues: 14.2664
Evaluate side-chains
  40 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  527 MET
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  738 VAL
Chi-restraints excluded: chain B residue  770 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 430 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.105813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.086530 restraints weight = 14204.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.79
r_work: 0.3462 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.6806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5928  Z= 0.156
  Angle     :  0.621  12.195   8058  Z= 0.302
  Chirality :  0.045   0.164    909
  Planarity :  0.004   0.041   1009
  Dihedral  :  8.742  88.531    854
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 23.93 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.84 (0.31), residues: 692
  helix:  1.03 (0.33), residues: 230
  sheet: -1.24 (0.40), residues: 158
  loop : -1.37 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 643 
 TYR   0.010   0.001   TYR B 313 
 PHE   0.009   0.001   PHE B 470 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 818 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 ( 5928)
  covalent geometry    : angle       0.62086 /  0.30 ( 8058)
  hydrogen bonds       : bond        0.03311 /  2.34 (  238)
  hydrogen bonds       : angle       5.25400 /  3.57 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1536.96 seconds
wall clock time: 27 minutes 7.81 seconds (1627.81 seconds total)