Starting phenix.real_space_refine
on Fri Aug 22 19:12:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2025/8i3q_35154.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      95      5.49       5
     S      12      5.16       5
     C    4057      2.51       5
     N    1312      2.21       5
     O    1521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6998
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 2026
          Classifications: {'RNA': 95}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 44, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 83}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4971
          Classifications: {'peptide': 595}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 556}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6549  SG  CYS A 711      29.245  14.332  41.891  1.00 82.48           S
  ATOM   6569  SG  CYS A 714      27.687  10.896  43.793  1.00 85.07           S
  ATOM   6757  SG  CYS A 735      31.613  10.871  41.848  1.00 98.72           S
  ATOM   6776  SG  CYS A 738      28.630  10.360  40.525  1.00 97.60           S

  Time building chain proxies: 1.54, per 1000 atoms: 0.22
  Number of scatterers: 6998
  At special positions: 0
  Unit cell: (85.68, 91.56, 99.96, 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)
     Zn      1     29.99
     S      12     16.00
     P      95     15.00
     O    1521      8.00
     N    1312      7.00
     C    4057      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: 0.42
  Conformation dependent library (CDL) restraints added in 225.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 738 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 711 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 735 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 714 "
      Number of angles added : 6


  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      50.6% alpha, 8.2% beta
      31 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 65
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 78 through 87
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.636A  pdb=" N   SER A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 113
    Processing helix  chain 'A' and resid 126 through 138
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 4.258A  pdb=" N   ASP A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 200
      removed outlier: 4.619A  pdb=" N   ARG A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ALA A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 200 " --> pdb=" O   TRP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
      removed outlier: 4.153A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 211 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ILE A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE A 215 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 367
      removed outlier: 3.526A  pdb=" N   GLU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.803A  pdb=" N   LEU A 470 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 499
      removed outlier: 4.523A  pdb=" N   LYS A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 595
      removed outlier: 3.515A  pdb=" N   HIS A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   SER A 585 " --> pdb=" O   ARG A 581 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   GLU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 647
      removed outlier: 3.851A  pdb=" N   ASN A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 669
      removed outlier: 3.533A  pdb=" N   ASP A 669 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 678
      removed outlier: 3.604A  pdb=" N   ARG A 674 " --> pdb=" O   GLU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.521A  pdb=" N   ILE A 684 " --> pdb=" O   ALA A 680 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 695 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 710
    Processing helix  chain 'A' and resid 722 through 729
      removed outlier: 3.998A  pdb=" N   LYS A 726 " --> pdb=" O   LYS A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 757
      removed outlier: 3.723A  pdb=" N   TRP A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 389
      removed outlier: 6.819A  pdb=" N   ARG A 453 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL A 439 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLY A 451 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LEU A 441 " --> pdb=" O   ARG A 449 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ARG A 449 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE A 443 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ARG A 447 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 402 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511
      removed outlier: 6.867A  pdb=" N   LEU A 510 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 652 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 654 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 524
      removed outlier: 4.032A  pdb=" N   GLN A 531 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.505A  pdb=" N   VAL A 538 " --> pdb=" O   TYR A 544 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    633 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      80 hydrogen bonds
      144 hydrogen bond angles
      0 basepair planarities
      31 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.55 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: 1385
        1.33 -     1.45: 2200
        1.45 -     1.57: 3566
        1.57 -     1.69: 188
        1.69 -     1.81: 17
  Bond restraints: 7356
  Sorted by residual:
  bond pdb=" N   LYS A  73 "
       pdb=" CA  LYS A  73 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.032 8.30e-03 1.45e+04 1.51e+01
  bond pdb=" CA  GLU A 391 "
       pdb=" C   GLU A 391 "
    ideal  model  delta    sigma   weight residual
    1.525  1.485  0.040 1.32e-02 5.74e+03 9.11e+00
  bond pdb=" N   LEU A 705 "
       pdb=" CA  LEU A 705 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.06e-02 8.90e+03 9.11e+00
  bond pdb=" N   VAL A 710 "
       pdb=" CA  VAL A 710 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.22e-02 6.72e+03 8.06e+00
  bond pdb=" N   ARG A 382 "
       pdb=" CA  ARG A 382 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.17e-02 7.31e+03 8.01e+00
  ... (remaining 7351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 10117
        2.45 -     4.91: 236
        4.91 -     7.36: 20
        7.36 -     9.81: 1
        9.81 -    12.27: 2
  Bond angle restraints: 10376
  Sorted by residual:
  angle pdb=" N   ALA A 482 "
        pdb=" CA  ALA A 482 "
        pdb=" C   ALA A 482 "
      ideal   model   delta    sigma   weight residual
     113.23  104.26    8.97 1.24e+00 6.50e-01 5.23e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  104.29    7.07 1.09e+00 8.42e-01 4.20e+01
  angle pdb=" CA  GLN A 483 "
        pdb=" CB  GLN A 483 "
        pdb=" CG  GLN A 483 "
      ideal   model   delta    sigma   weight residual
     114.10  123.92   -9.82 2.00e+00 2.50e-01 2.41e+01
  angle pdb=" C   PHE A 478 "
        pdb=" N   PRO A 479 "
        pdb=" CA  PRO A 479 "
      ideal   model   delta    sigma   weight residual
     119.84  114.25    5.59 1.25e+00 6.40e-01 2.00e+01
  angle pdb=" C   ARG A  47 "
        pdb=" N   LYS A  48 "
        pdb=" CA  LYS A  48 "
      ideal   model   delta    sigma   weight residual
     120.44  126.05   -5.61 1.30e+00 5.92e-01 1.86e+01
  ... (remaining 10371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 4206
       34.82 -    69.63: 349
       69.63 -   104.45: 45
      104.45 -   139.27: 5
      139.27 -   174.08: 5
  Dihedral angle restraints: 4610
    sinusoidal: 2866
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" CD  ARG A 382 "
           pdb=" NE  ARG A 382 "
           pdb=" CZ  ARG A 382 "
           pdb=" NH1 ARG A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.76  -88.76     1      1.00e+01 1.00e-02 9.39e+01
  dihedral pdb=" O4'   C C  38 "
           pdb=" C1'   C C  38 "
           pdb=" N1    C C  38 "
           pdb=" C2    C C  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    9.75 -169.75     1      1.50e+01 4.44e-03 8.47e+01
  dihedral pdb=" O4'   U C  55 "
           pdb=" C1'   U C  55 "
           pdb=" N1    U C  55 "
           pdb=" C2    U C  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   48.63  151.37     1      1.50e+01 4.44e-03 8.01e+01
  ... (remaining 4607 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1030
       0.068 -    0.135: 103
       0.135 -    0.203: 27
       0.203 -    0.270: 4
       0.270 -    0.338: 3
  Chirality restraints: 1167
  Sorted by residual:
  chirality pdb=" CA  PHE A 398 "
            pdb=" N   PHE A 398 "
            pdb=" C   PHE A 398 "
            pdb=" CB  PHE A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  ASN A  42 "
            pdb=" N   ASN A  42 "
            pdb=" C   ASN A  42 "
            pdb=" CB  ASN A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  CYS A 714 "
            pdb=" N   CYS A 714 "
            pdb=" C   CYS A 714 "
            pdb=" CB  CYS A 714 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 1164 not shown)

  Planarity restraints: 1002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 382 "    1.099 9.50e-02 1.11e+02   4.93e-01 1.46e+02
        pdb=" NE  ARG A 382 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 382 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 382 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 382 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 462 "   -0.328 9.50e-02 1.11e+02   1.47e-01 1.32e+01
        pdb=" NE  ARG A 462 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 462 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 462 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 462 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 714 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.17e+00
        pdb=" C   CYS A 714 "    0.049 2.00e-02 2.50e+03
        pdb=" O   CYS A 714 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ARG A 715 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 999 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 17
        2.39 -     3.02: 3754
        3.02 -     3.64: 11191
        3.64 -     4.27: 16937
        4.27 -     4.90: 25742
  Nonbonded interactions: 57641
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 723 "
            pdb=" NZ  LYS A 734 "
     model   vdw
     1.762 3.200
  nonbonded pdb=" O2'   G C  74 "
            pdb=" O5'   A C  75 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" NE2 GLN A  52 "
            pdb=" OH  TYR A 155 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" NH1 ARG A 754 "
            pdb=" OE1 GLU A 759 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O2'   A C  76 "
            pdb=" OP1   G C  77 "
     model   vdw
     2.279 3.040
  ... (remaining 57636 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:             0.900
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.470
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
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      :  0.007   0.207   7360  Z= 0.354
  Angle     :  0.894  20.646  10382  Z= 0.514
  Chirality :  0.049   0.338   1167
  Planarity :  0.017   0.493   1002
  Dihedral  : 22.354 174.081   3470
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  :  4.43 %
    Favored  : 90.17 %
  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 aren not related in a simple way.
  whole:  0.08 (0.34), residues: 585
  helix:  1.56 (0.31), residues: 267
  sheet: -0.12 (0.62), residues: 70
  loop : -1.64 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.013   0.002   TYR A  18 
 PHE   0.016   0.002   PHE A 398 
 TRP   0.028   0.002   TRP A 632 
 HIS   0.004   0.001   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7356)
  covalent geometry    : angle       0.82887 (10376)
  hydrogen bonds       : bond        0.16786 (  301)
  hydrogen bonds       : angle       5.90318 (  777)
  metal coordination   : bond        0.19495 (    4)
  metal coordination   : angle      13.92871 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  570 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6653 (mtp-110)
  outliers start: 28
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1731
  time to fit residues: 21.0608
Evaluate side-chains
  42 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  483 GLN
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  517 ASP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  738 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 159 HIS
A 383 HIS
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.134689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.101367 restraints weight = 12164.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.97
r_work: 0.3322 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   7360  Z= 0.312
  Angle     :  0.832   9.262  10382  Z= 0.425
  Chirality :  0.047   0.252   1167
  Planarity :  0.008   0.072   1002
  Dihedral  : 22.687 178.991   2169
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 10.60 %
    Favored  : 86.13 %
  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 aren not related in a simple way.
  whole: -0.04 (0.34), residues: 585
  helix:  1.41 (0.29), residues: 259
  sheet: -0.94 (0.58), residues: 75
  loop : -1.26 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 480 
 TYR   0.015   0.003   TYR A 665 
 PHE   0.024   0.003   PHE A  50 
 TRP   0.018   0.003   TRP A 632 
 HIS   0.007   0.002   HIS A 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 ( 7356)
  covalent geometry    : angle       0.82359 (10376)
  hydrogen bonds       : bond        0.07597 (  301)
  hydrogen bonds       : angle       4.29826 (  777)
  metal coordination   : bond        0.00694 (    4)
  metal coordination   : angle       4.95728 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  144 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7296 (mt-10)
  outliers start: 17
  outliers final: 9
  residues processed: 50
  average time/residue: 0.1317
  time to fit residues: 8.1190
Evaluate side-chains
  36 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  631 ASP
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.136697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.104322 restraints weight = 11983.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.94
r_work: 0.3378 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7360  Z= 0.149
  Angle     :  0.627   7.406  10382  Z= 0.322
  Chirality :  0.039   0.223   1167
  Planarity :  0.005   0.051   1002
  Dihedral  : 22.288 178.240   2152
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.52 %
    Favored  : 85.16 %
  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 aren not related in a simple way.
  whole:  0.61 (0.35), residues: 585
  helix:  2.11 (0.29), residues: 259
  sheet: -0.75 (0.61), residues: 69
  loop : -1.08 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.014   0.002   PHE A  81 
 TRP   0.015   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7356)
  covalent geometry    : angle       0.62483 (10376)
  hydrogen bonds       : bond        0.05386 (  301)
  hydrogen bonds       : angle       3.81741 (  777)
  metal coordination   : bond        0.00341 (    4)
  metal coordination   : angle       2.37581 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  371 ARG cc_start: 0.8282 (tpm170) cc_final: 0.8003 (mmp80)
REVERT: A  577 LEU cc_start: 0.8561 (mt) cc_final: 0.8344 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1134
  time to fit residues: 5.9072
Evaluate side-chains
  32 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0060
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 159 HIS
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.140333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.108700 restraints weight = 12118.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.93
r_work: 0.3451 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7360  Z= 0.105
  Angle     :  0.565   7.424  10382  Z= 0.287
  Chirality :  0.036   0.221   1167
  Planarity :  0.004   0.047   1002
  Dihedral  : 22.123 178.308   2148
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.64 %
    Favored  : 84.39 %
  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 aren not related in a simple way.
  whole:  1.19 (0.36), residues: 585
  helix:  2.68 (0.30), residues: 257
  sheet: -0.45 (0.59), residues: 74
  loop : -0.86 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  17 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.010   0.001   PHE A 756 
 TRP   0.017   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 7356)
  covalent geometry    : angle       0.56397 (10376)
  hydrogen bonds       : bond        0.04170 (  301)
  hydrogen bonds       : angle       3.49154 (  777)
  metal coordination   : bond        0.00236 (    4)
  metal coordination   : angle       1.72933 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  371 ARG cc_start: 0.8195 (tpm170) cc_final: 0.7989 (mmp80)
  outliers start: 5
  outliers final: 3
  residues processed: 32
  average time/residue: 0.1347
  time to fit residues: 5.2209
Evaluate side-chains
  24 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 36 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8322

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.139588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.107816 restraints weight = 12110.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.92
r_work: 0.3422 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7360  Z= 0.112
  Angle     :  0.565   7.487  10382  Z= 0.287
  Chirality :  0.036   0.220   1167
  Planarity :  0.004   0.045   1002
  Dihedral  : 22.034 177.937   2148
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.03 %
    Favored  : 83.24 %
  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 aren not related in a simple way.
  whole:  1.32 (0.36), residues: 585
  helix:  2.81 (0.30), residues: 257
  sheet: -0.32 (0.59), residues: 76
  loop : -0.83 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.014   0.001   PHE A  50 
 TRP   0.018   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7356)
  covalent geometry    : angle       0.56335 (10376)
  hydrogen bonds       : bond        0.04522 (  301)
  hydrogen bonds       : angle       3.49805 (  777)
  metal coordination   : bond        0.00222 (    4)
  metal coordination   : angle       1.77326 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7355 (mmm-85)
REVERT: A  371 ARG cc_start: 0.8217 (tpm170) cc_final: 0.7996 (mmp80)
  outliers start: 9
  outliers final: 5
  residues processed: 34
  average time/residue: 0.1584
  time to fit residues: 6.6144
Evaluate side-chains
  29 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0170
   chunk 5 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.4020

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.137919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.105933 restraints weight = 12235.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.93
r_work: 0.3385 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7360  Z= 0.136
  Angle     :  0.587   7.483  10382  Z= 0.299
  Chirality :  0.037   0.219   1167
  Planarity :  0.005   0.047   1002
  Dihedral  : 22.081 177.813   2148
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.61 %
    Favored  : 82.66 %
  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 aren not related in a simple way.
  whole:  1.19 (0.36), residues: 585
  helix:  2.66 (0.30), residues: 258
  sheet: -0.32 (0.60), residues: 76
  loop : -0.90 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.014   0.002   PHE A  50 
 TRP   0.017   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7356)
  covalent geometry    : angle       0.58589 (10376)
  hydrogen bonds       : bond        0.04885 (  301)
  hydrogen bonds       : angle       3.60419 (  777)
  metal coordination   : bond        0.00221 (    4)
  metal coordination   : angle       1.83689 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7384 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7251 (tt)
REVERT: A  371 ARG cc_start: 0.8209 (tpm170) cc_final: 0.8000 (mmp80)
  outliers start: 9
  outliers final: 5
  residues processed: 34
  average time/residue: 0.1413
  time to fit residues: 5.9243
Evaluate side-chains
  31 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.137526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.106020 restraints weight = 12021.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.90
r_work: 0.3393 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.4387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7360  Z= 0.132
  Angle     :  0.584   7.486  10382  Z= 0.297
  Chirality :  0.036   0.219   1167
  Planarity :  0.004   0.047   1002
  Dihedral  : 22.046 178.741   2148
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.80 %
    Favored  : 82.27 %
  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 aren not related in a simple way.
  whole:  1.23 (0.36), residues: 585
  helix:  2.68 (0.30), residues: 259
  sheet: -0.30 (0.60), residues: 76
  loop : -0.87 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.013   0.002   PHE A  50 
 TRP   0.017   0.002   TRP A 632 
 HIS   0.002   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7356)
  covalent geometry    : angle       0.58236 (10376)
  hydrogen bonds       : bond        0.04786 (  301)
  hydrogen bonds       : angle       3.55554 (  777)
  metal coordination   : bond        0.00247 (    4)
  metal coordination   : angle       1.95047 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7353 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7266 (tt)
REVERT: A  733 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5657 (p90)
REVERT: A  734 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7600 (ttmm)
  outliers start: 10
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1248
  time to fit residues: 6.3308
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  733 PHE
Chi-restraints excluded: chain A residue  734 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.134508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.102384 restraints weight = 12103.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.95
r_work: 0.3323 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.4549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7360  Z= 0.182
  Angle     :  0.654  14.978  10382  Z= 0.326
  Chirality :  0.039   0.220   1167
  Planarity :  0.005   0.048   1002
  Dihedral  : 22.089 179.678   2148
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.57 %
    Favored  : 81.31 %
  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 aren not related in a simple way.
  whole:  0.99 (0.35), residues: 585
  helix:  2.44 (0.30), residues: 260
  sheet: -0.47 (0.59), residues: 77
  loop : -0.95 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  17 
 TYR   0.012   0.002   TYR A 359 
 PHE   0.017   0.002   PHE A  50 
 TRP   0.017   0.002   TRP A 632 
 HIS   0.005   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7356)
  covalent geometry    : angle       0.65180 (10376)
  hydrogen bonds       : bond        0.05604 (  301)
  hydrogen bonds       : angle       3.74197 (  777)
  metal coordination   : bond        0.00286 (    4)
  metal coordination   : angle       2.49311 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7445 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7471 (tt)
REVERT: A  733 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5894 (p90)
  outliers start: 11
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1230
  time to fit residues: 5.8079
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  733 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0040
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.137997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.106315 restraints weight = 12130.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.94
r_work: 0.3397 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7360  Z= 0.108
  Angle     :  0.593  16.402  10382  Z= 0.291
  Chirality :  0.036   0.221   1167
  Planarity :  0.004   0.049   1002
  Dihedral  : 22.037 178.908   2148
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 16.96 %
    Favored  : 81.89 %
  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 aren not related in a simple way.
  whole:  1.37 (0.36), residues: 585
  helix:  2.83 (0.30), residues: 259
  sheet: -0.20 (0.61), residues: 76
  loop : -0.85 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.010   0.001   PHE A  50 
 TRP   0.019   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7356)
  covalent geometry    : angle       0.59142 (10376)
  hydrogen bonds       : bond        0.04276 (  301)
  hydrogen bonds       : angle       3.43796 (  777)
  metal coordination   : bond        0.00235 (    4)
  metal coordination   : angle       1.82826 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7304 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7269 (tt)
  outliers start: 6
  outliers final: 3
  residues processed: 34
  average time/residue: 0.1180
  time to fit residues: 5.0748
Evaluate side-chains
  29 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.135889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.103865 restraints weight = 12046.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.93
r_work: 0.3354 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7360  Z= 0.135
  Angle     :  0.616  17.187  10382  Z= 0.303
  Chirality :  0.037   0.219   1167
  Planarity :  0.005   0.098   1002
  Dihedral  : 22.021 179.063   2148
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 17.73 %
    Favored  : 81.31 %
  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 aren not related in a simple way.
  whole:  1.28 (0.36), residues: 585
  helix:  2.71 (0.30), residues: 260
  sheet: -0.20 (0.61), residues: 76
  loop : -0.87 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 695 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.014   0.002   PHE A  50 
 TRP   0.020   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7356)
  covalent geometry    : angle       0.61441 (10376)
  hydrogen bonds       : bond        0.04888 (  301)
  hydrogen bonds       : angle       3.56208 (  777)
  metal coordination   : bond        0.00241 (    4)
  metal coordination   : angle       2.06837 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7369 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7273 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 34
  average time/residue: 0.1439
  time to fit residues: 6.1232
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.135930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.104123 restraints weight = 12041.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.91
r_work: 0.3355 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7360  Z= 0.134
  Angle     :  0.617  17.206  10382  Z= 0.303
  Chirality :  0.037   0.219   1167
  Planarity :  0.005   0.089   1002
  Dihedral  : 22.031 179.983   2148
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 18.11 %
    Favored  : 80.73 %
  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 aren not related in a simple way.
  whole:  1.23 (0.36), residues: 585
  helix:  2.65 (0.30), residues: 260
  sheet: -0.27 (0.61), residues: 77
  loop : -0.87 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 224 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.013   0.002   PHE A  50 
 TRP   0.020   0.002   TRP A 632 
 HIS   0.002   0.001   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7356)
  covalent geometry    : angle       0.61473 (10376)
  hydrogen bonds       : bond        0.04814 (  301)
  hydrogen bonds       : angle       3.55959 (  777)
  metal coordination   : bond        0.00267 (    4)
  metal coordination   : angle       2.14919 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.21 seconds
wall clock time: 25 minutes 32.80 seconds (1532.80 seconds total)