Starting phenix.real_space_refine
on Mon Sep 23 18:21:33 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/09_2024/5ms1_3562.cif"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2774      2.51       5
     N     732      2.21       5
     O     814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 4350
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1501
          Classifications: {'peptide': 189}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 170}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2849
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 14, 'TRANS': 352}
  Time building chain proxies: 5.15, per 1000 atoms: 1.18
  Number of scatterers: 4350
  At special positions: 0
  Unit cell: (89.1, 85.8, 91.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     814      8.00
     N     732      7.00
     C    2774      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: 1.44
  Conformation dependent library (CDL) restraints added in 690.1 milliseconds
  

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1034

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      12.9% alpha, 46.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 61
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 58 through 63
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 277 through 281
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.522A  pdb=" N   ASP B 321 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA A  63 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASN A 174 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41
      removed outlier: 3.734A  pdb=" N   ARG A 106 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32
      removed outlier: 6.017A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46
      removed outlier: 5.691A  pdb=" N   VAL B  41 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   CYS B 152 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   CYS B  87 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP B 111 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214

    179 hydrogen bonds defined for protein.
    447 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: 1.29

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1009
        1.32 -     1.45: 1181
        1.45 -     1.57: 2226
        1.57 -     1.69: 0
        1.69 -     1.82: 47
  Bond restraints: 4463
  Sorted by residual:
  bond pdb=" N   PRO B 282 "
       pdb=" CA  PRO B 282 "
    ideal  model  delta    sigma   weight residual
    1.467  1.415  0.052 1.21e-02 6.83e+03 1.83e+01
  bond pdb=" N   PRO A 181 "
       pdb=" CA  PRO A 181 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.048 1.19e-02 7.06e+03 1.59e+01
  bond pdb=" N   PRO A  41 "
       pdb=" CA  PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.466  1.420  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" N   PRO A  13 "
       pdb=" CA  PRO A  13 "
    ideal  model  delta    sigma   weight residual
    1.467  1.421  0.046 1.21e-02 6.83e+03 1.44e+01
  bond pdb=" N   PRO B 214 "
       pdb=" CA  PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.467  1.423  0.044 1.21e-02 6.83e+03 1.34e+01
  ... (remaining 4458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4935
        1.69 -     3.37: 873
        3.37 -     5.06: 177
        5.06 -     6.74: 69
        6.74 -     8.43: 20
  Bond angle restraints: 6074
  Sorted by residual:
  angle pdb=" CA  ARG A  77 "
        pdb=" C   ARG A  77 "
        pdb=" O   ARG A  77 "
      ideal   model   delta    sigma   weight residual
     120.71  113.89    6.82 1.06e+00 8.90e-01 4.15e+01
  angle pdb=" C   PRO A  20 "
        pdb=" N   PRO A  21 "
        pdb=" CA  PRO A  21 "
      ideal   model   delta    sigma   weight residual
     120.03  126.37   -6.34 9.90e-01 1.02e+00 4.10e+01
  angle pdb=" C   GLY A 126 "
        pdb=" N   PRO A 127 "
        pdb=" CA  PRO A 127 "
      ideal   model   delta    sigma   weight residual
     119.64  125.65   -6.01 1.01e+00 9.80e-01 3.54e+01
  angle pdb=" C   PRO A  54 "
        pdb=" N   PRO A  55 "
        pdb=" CA  PRO A  55 "
      ideal   model   delta    sigma   weight residual
     119.32  125.73   -6.41 1.14e+00 7.69e-01 3.17e+01
  angle pdb=" C   THR A  19 "
        pdb=" N   PRO A  20 "
        pdb=" CA  PRO A  20 "
      ideal   model   delta    sigma   weight residual
     119.66  123.52   -3.86 7.30e-01 1.88e+00 2.79e+01
  ... (remaining 6069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 2555
       16.74 -    33.48: 41
       33.48 -    50.22: 15
       50.22 -    66.96: 9
       66.96 -    83.70: 4
  Dihedral angle restraints: 2624
    sinusoidal: 1022
      harmonic: 1602
  Sorted by residual:
  dihedral pdb=" CA  ARG A  77 "
           pdb=" C   ARG A  77 "
           pdb=" N   GLY A  78 "
           pdb=" CA  GLY A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   37.92  -37.92     0      5.00e+00 4.00e-02 5.75e+01
  dihedral pdb=" CG  ARG A 154 "
           pdb=" CD  ARG A 154 "
           pdb=" NE  ARG A 154 "
           pdb=" CZ  ARG A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.34   40.34     2      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CA  ASP A 166 "
           pdb=" CB  ASP A 166 "
           pdb=" CG  ASP A 166 "
           pdb=" OD1 ASP A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.90   50.90     1      2.00e+01 2.50e-03 8.86e+00
  ... (remaining 2621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 410
       0.058 -    0.117: 199
       0.117 -    0.175: 51
       0.175 -    0.234: 12
       0.234 -    0.292: 1
  Chirality restraints: 673
  Sorted by residual:
  chirality pdb=" CA  MET B 231 "
            pdb=" N   MET B 231 "
            pdb=" C   MET B 231 "
            pdb=" CB  MET B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  SER B 309 "
            pdb=" N   SER B 309 "
            pdb=" C   SER B 309 "
            pdb=" CB  SER B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU B 184 "
            pdb=" N   LEU B 184 "
            pdb=" C   LEU B 184 "
            pdb=" CB  LEU B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 670 not shown)

  Planarity restraints: 782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  77 "    0.059 2.00e-02 2.50e+03   1.20e-01 1.43e+02
        pdb=" C   ARG A  77 "   -0.207 2.00e-02 2.50e+03
        pdb=" O   ARG A  77 "    0.077 2.00e-02 2.50e+03
        pdb=" N   GLY A  78 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "   -0.036 2.00e-02 2.50e+03   1.74e-02 7.60e+00
        pdb=" CG  TRP A  47 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 130 "    0.036 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO B 131 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 131 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 131 "    0.031 5.00e-02 4.00e+02
  ... (remaining 779 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1966
        2.91 -     3.41: 3911
        3.41 -     3.91: 7317
        3.91 -     4.40: 8459
        4.40 -     4.90: 13903
  Nonbonded interactions: 35556
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 279 "
            pdb=" OE1 GLU B 279 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" OG  SER B 366 "
            pdb=" N   ARG B 367 "
     model   vdw
     2.438 3.120
  nonbonded pdb=" O   SER A 183 "
            pdb=" OG1 THR A 184 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" N   GLU A 101 "
            pdb=" OE1 GLU A 101 "
     model   vdw
     2.442 3.120
  nonbonded pdb=" OG1 THR B 224 "
            pdb=" N   GLN B 225 "
     model   vdw
     2.474 3.120
  ... (remaining 35551 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.750
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.770
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
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      :  0.014   0.058   4463  Z= 0.906
  Angle     :  1.510   8.431   6074  Z= 1.007
  Chirality :  0.071   0.292    673
  Planarity :  0.008   0.120    782
  Dihedral  :  9.301  83.699   1590
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  5.45 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.34), residues: 550
  helix: -3.05 (0.45), residues: 53
  sheet:  1.15 (0.36), residues: 192
  loop : -1.24 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.006   TRP A  47 
 HIS   0.004   0.001   HIS A  50 
 PHE   0.026   0.004   PHE B 125 
 TYR   0.021   0.005   TYR B 278 
 ARG   0.004   0.001   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   20 PRO cc_start: 0.9118 (Cg_exo) cc_final: 0.8803 (Cg_endo)
REVERT: A   39 ILE cc_start: 0.8932 (mt) cc_final: 0.8720 (mt)
REVERT: A   49 THR cc_start: 0.9359 (p) cc_final: 0.9002 (t)
REVERT: A   75 ASN cc_start: 0.7730 (m-40) cc_final: 0.7429 (m-40)
REVERT: A   82 LYS cc_start: 0.8103 (mttt) cc_final: 0.7096 (mmmt)
REVERT: A  113 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8540 (Cg_endo)
REVERT: A  195 ARG cc_start: 0.5271 (mtm-85) cc_final: 0.5049 (mtt180)
REVERT: B   31 LEU cc_start: 0.8037 (tp) cc_final: 0.7695 (tt)
REVERT: B   87 CYS cc_start: 0.8880 (t) cc_final: 0.8182 (t)
REVERT: B  111 ASP cc_start: 0.8767 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  116 ASN cc_start: 0.8548 (t0) cc_final: 0.8107 (t0)
REVERT: B  134 ASP cc_start: 0.7940 (p0) cc_final: 0.7696 (p0)
REVERT: B  152 CYS cc_start: 0.7941 (t) cc_final: 0.7079 (t)
REVERT: B  153 VAL cc_start: 0.8200 (t) cc_final: 0.7910 (t)
REVERT: B  259 LYS cc_start: 0.8547 (mttt) cc_final: 0.6947 (pttp)
REVERT: B  261 THR cc_start: 0.8227 (m) cc_final: 0.7930 (p)
REVERT: B  351 ILE cc_start: 0.7416 (mt) cc_final: 0.7107 (mt)
REVERT: B  353 ASP cc_start: 0.8361 (t0) cc_final: 0.8037 (t0)
REVERT: B  360 ASN cc_start: 0.9000 (t0) cc_final: 0.8683 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1752
  time to fit residues: 36.8216
Evaluate side-chains
  100 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 119 ASN
A 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4463  Z= 0.272
  Angle     :  0.638   7.336   6074  Z= 0.345
  Chirality :  0.047   0.160    673
  Planarity :  0.006   0.043    782
  Dihedral  :  4.796  19.951    594
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.64 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.34), residues: 550
  helix: -1.62 (0.69), residues: 48
  sheet:  0.99 (0.37), residues: 195
  loop : -0.77 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  47 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.020   0.002   PHE B 275 
 TYR   0.012   0.002   TYR B 241 
 ARG   0.004   0.001   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8410 (mttt) cc_final: 0.7481 (mmmt)
REVERT: A  112 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8712 (tt0)
REVERT: A  113 PRO cc_start: 0.9112 (Cg_exo) cc_final: 0.8812 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8196 (tt) cc_final: 0.7923 (tt)
REVERT: B   87 CYS cc_start: 0.8997 (t) cc_final: 0.8614 (t)
REVERT: B   92 ILE cc_start: 0.9222 (mm) cc_final: 0.9019 (mp)
REVERT: B   99 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8178 (mtmm)
REVERT: B  102 THR cc_start: 0.8884 (p) cc_final: 0.8633 (t)
REVERT: B  109 SER cc_start: 0.8635 (p) cc_final: 0.8400 (t)
REVERT: B  116 ASN cc_start: 0.9155 (t0) cc_final: 0.8702 (t0)
REVERT: B  132 CYS cc_start: 0.9083 (p) cc_final: 0.8495 (p)
REVERT: B  225 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8252 (mm-40)
REVERT: B  239 TRP cc_start: 0.8934 (m-90) cc_final: 0.8367 (m100)
REVERT: B  259 LYS cc_start: 0.8597 (mttt) cc_final: 0.6988 (pttp)
REVERT: B  271 LEU cc_start: 0.8738 (tp) cc_final: 0.8365 (tt)
REVERT: B  353 ASP cc_start: 0.8605 (t0) cc_final: 0.8139 (t0)
REVERT: B  360 ASN cc_start: 0.9184 (t0) cc_final: 0.8818 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1257
  time to fit residues: 22.3714
Evaluate side-chains
  108 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B 128 ASN
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   4463  Z= 0.393
  Angle     :  0.709   8.015   6074  Z= 0.379
  Chirality :  0.048   0.158    673
  Planarity :  0.005   0.047    782
  Dihedral  :  4.861  17.310    594
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.64 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.87 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.34), residues: 550
  helix: -1.43 (0.64), residues: 52
  sheet:  0.97 (0.38), residues: 193
  loop : -0.92 (0.32), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 170 
 HIS   0.004   0.001   HIS B 331 
 PHE   0.019   0.003   PHE B 202 
 TYR   0.020   0.002   TYR B 241 
 ARG   0.005   0.001   ARG A 193 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8633 (mttt) cc_final: 0.8015 (mmmt)
REVERT: A  112 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8674 (tt0)
REVERT: A  113 PRO cc_start: 0.9105 (Cg_exo) cc_final: 0.8782 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8461 (tt) cc_final: 0.8168 (tt)
REVERT: B   43 LEU cc_start: 0.8845 (tp) cc_final: 0.8599 (tp)
REVERT: B   99 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8352 (mtmm)
REVERT: B  102 THR cc_start: 0.8938 (p) cc_final: 0.8679 (t)
REVERT: B  110 GLN cc_start: 0.8724 (tt0) cc_final: 0.8134 (tm-30)
REVERT: B  116 ASN cc_start: 0.9426 (t0) cc_final: 0.9104 (t0)
REVERT: B  132 CYS cc_start: 0.9077 (p) cc_final: 0.8793 (p)
REVERT: B  134 ASP cc_start: 0.8374 (p0) cc_final: 0.8067 (p0)
REVERT: B  152 CYS cc_start: 0.8388 (t) cc_final: 0.7312 (t)
REVERT: B  178 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8617 (mt-10)
REVERT: B  206 VAL cc_start: 0.8570 (m) cc_final: 0.8282 (p)
REVERT: B  231 MET cc_start: 0.8892 (tmm) cc_final: 0.8579 (tmm)
REVERT: B  259 LYS cc_start: 0.8761 (mttt) cc_final: 0.7181 (pttp)
REVERT: B  271 LEU cc_start: 0.8827 (tp) cc_final: 0.8358 (tt)
REVERT: B  298 VAL cc_start: 0.9192 (t) cc_final: 0.8984 (m)
REVERT: B  353 ASP cc_start: 0.8673 (t0) cc_final: 0.8273 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1244
  time to fit residues: 18.5312
Evaluate side-chains
  92 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4463  Z= 0.314
  Angle     :  0.644   6.822   6074  Z= 0.342
  Chirality :  0.047   0.150    673
  Planarity :  0.005   0.045    782
  Dihedral  :  4.752  19.777    594
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.35), residues: 550
  helix: -1.65 (0.63), residues: 54
  sheet:  0.91 (0.38), residues: 193
  loop : -0.93 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 196 
 HIS   0.003   0.001   HIS B 247 
 PHE   0.022   0.002   PHE A 165 
 TYR   0.016   0.002   TYR B 278 
 ARG   0.006   0.001   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.9211 (mtm180) cc_final: 0.8932 (mtm-85)
REVERT: A   69 THR cc_start: 0.9178 (m) cc_final: 0.8813 (p)
REVERT: A   82 LYS cc_start: 0.8750 (mttt) cc_final: 0.8012 (mmmt)
REVERT: A   87 ASP cc_start: 0.8755 (p0) cc_final: 0.8359 (p0)
REVERT: A  112 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8709 (tt0)
REVERT: A  113 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8311 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8171 (tt) cc_final: 0.7955 (tt)
REVERT: A  155 GLN cc_start: 0.9100 (mt0) cc_final: 0.8442 (mt0)
REVERT: A  166 ASP cc_start: 0.8952 (t70) cc_final: 0.8112 (t70)
REVERT: B   43 LEU cc_start: 0.8911 (tp) cc_final: 0.8644 (tp)
REVERT: B   82 ASP cc_start: 0.8743 (m-30) cc_final: 0.8520 (m-30)
REVERT: B   99 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8292 (mtmm)
REVERT: B  110 GLN cc_start: 0.8588 (tt0) cc_final: 0.8232 (tm-30)
REVERT: B  113 MET cc_start: 0.7970 (ptt) cc_final: 0.7727 (tpp)
REVERT: B  132 CYS cc_start: 0.9058 (p) cc_final: 0.8817 (p)
REVERT: B  134 ASP cc_start: 0.8432 (p0) cc_final: 0.8124 (p0)
REVERT: B  152 CYS cc_start: 0.8439 (t) cc_final: 0.7383 (t)
REVERT: B  178 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8716 (mt-10)
REVERT: B  206 VAL cc_start: 0.8795 (m) cc_final: 0.8528 (p)
REVERT: B  259 LYS cc_start: 0.9027 (mttt) cc_final: 0.7399 (pttp)
REVERT: B  271 LEU cc_start: 0.8727 (tp) cc_final: 0.8150 (tt)
REVERT: B  321 ASP cc_start: 0.9101 (t0) cc_final: 0.8709 (t0)
REVERT: B  353 ASP cc_start: 0.8693 (t0) cc_final: 0.8267 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1551
  time to fit residues: 23.0061
Evaluate side-chains
  93 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0470
   chunk 26 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.6084

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 158 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.5869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4463  Z= 0.280
  Angle     :  0.601   6.449   6074  Z= 0.319
  Chirality :  0.046   0.148    673
  Planarity :  0.005   0.048    782
  Dihedral  :  4.571  17.186    594
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.64 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.35), residues: 550
  helix: -1.42 (0.70), residues: 47
  sheet:  0.99 (0.39), residues: 187
  loop : -0.93 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 170 
 HIS   0.002   0.001   HIS B 283 
 PHE   0.015   0.002   PHE B 275 
 TYR   0.008   0.001   TYR B 278 
 ARG   0.004   0.000   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.9187 (mtm180) cc_final: 0.8979 (mtm-85)
REVERT: A   69 THR cc_start: 0.9194 (m) cc_final: 0.8843 (p)
REVERT: A   82 LYS cc_start: 0.8757 (mttt) cc_final: 0.8096 (mmmt)
REVERT: A  112 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8732 (tt0)
REVERT: A  113 PRO cc_start: 0.8676 (Cg_exo) cc_final: 0.8329 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8189 (tt) cc_final: 0.7986 (tt)
REVERT: A  166 ASP cc_start: 0.8950 (t70) cc_final: 0.8093 (t70)
REVERT: B   43 LEU cc_start: 0.8907 (tp) cc_final: 0.8653 (tp)
REVERT: B  110 GLN cc_start: 0.8648 (tt0) cc_final: 0.8359 (tm-30)
REVERT: B  116 ASN cc_start: 0.9489 (t0) cc_final: 0.8923 (t0)
REVERT: B  132 CYS cc_start: 0.9003 (p) cc_final: 0.8800 (p)
REVERT: B  152 CYS cc_start: 0.8415 (t) cc_final: 0.7548 (t)
REVERT: B  178 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8744 (mt-10)
REVERT: B  189 ASN cc_start: 0.8938 (m-40) cc_final: 0.8287 (t0)
REVERT: B  206 VAL cc_start: 0.8846 (m) cc_final: 0.8560 (p)
REVERT: B  253 MET cc_start: 0.9218 (mtm) cc_final: 0.8947 (mtm)
REVERT: B  321 ASP cc_start: 0.9036 (t0) cc_final: 0.8692 (t0)
REVERT: B  353 ASP cc_start: 0.8780 (t0) cc_final: 0.8320 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1420
  time to fit residues: 20.1215
Evaluate side-chains
  85 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 52 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0170
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   4463  Z= 0.157
  Angle     :  0.547   6.408   6074  Z= 0.288
  Chirality :  0.045   0.146    673
  Planarity :  0.004   0.049    782
  Dihedral  :  4.276  17.452    594
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.00 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.36), residues: 550
  helix: -1.48 (0.67), residues: 53
  sheet:  0.99 (0.39), residues: 189
  loop : -0.88 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 170 
 HIS   0.002   0.001   HIS B 331 
 PHE   0.015   0.002   PHE B 275 
 TYR   0.026   0.001   TYR B 278 
 ARG   0.003   0.000   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9123 (m100) cc_final: 0.8298 (m100)
REVERT: A   69 THR cc_start: 0.9087 (m) cc_final: 0.8791 (p)
REVERT: A   82 LYS cc_start: 0.8786 (mttt) cc_final: 0.8133 (mmmt)
REVERT: A  112 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8743 (tt0)
REVERT: A  113 PRO cc_start: 0.8697 (Cg_exo) cc_final: 0.8360 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8004 (tt) cc_final: 0.7632 (tt)
REVERT: A  166 ASP cc_start: 0.8765 (t70) cc_final: 0.7892 (t70)
REVERT: B   43 LEU cc_start: 0.8835 (tp) cc_final: 0.8525 (tp)
REVERT: B  100 TYR cc_start: 0.8733 (p90) cc_final: 0.8347 (p90)
REVERT: B  110 GLN cc_start: 0.8452 (tt0) cc_final: 0.8182 (tm-30)
REVERT: B  116 ASN cc_start: 0.9455 (t0) cc_final: 0.8969 (t0)
REVERT: B  132 CYS cc_start: 0.8997 (p) cc_final: 0.8782 (p)
REVERT: B  152 CYS cc_start: 0.8558 (t) cc_final: 0.7876 (t)
REVERT: B  206 VAL cc_start: 0.8832 (m) cc_final: 0.8577 (p)
REVERT: B  271 LEU cc_start: 0.8806 (tp) cc_final: 0.8036 (tt)
REVERT: B  279 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8639 (mm-30)
REVERT: B  321 ASP cc_start: 0.8981 (t0) cc_final: 0.8764 (t0)
REVERT: B  353 ASP cc_start: 0.8797 (t0) cc_final: 0.8355 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1600
  time to fit residues: 22.7370
Evaluate side-chains
  87 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.6510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   4463  Z= 0.454
  Angle     :  0.691   8.349   6074  Z= 0.362
  Chirality :  0.048   0.145    673
  Planarity :  0.005   0.051    782
  Dihedral  :  4.753  16.950    594
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.36), residues: 550
  helix: -1.64 (0.66), residues: 53
  sheet:  0.83 (0.39), residues: 189
  loop : -0.95 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 170 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.023   0.003   PHE B 202 
 TYR   0.009   0.002   TYR A  93 
 ARG   0.003   0.001   ARG B  97 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   69 THR cc_start: 0.9242 (m) cc_final: 0.8895 (p)
REVERT: A   82 LYS cc_start: 0.8792 (mttt) cc_final: 0.8166 (mmmt)
REVERT: A   98 MET cc_start: 0.9394 (mmp) cc_final: 0.9186 (mmm)
REVERT: A  108 PHE cc_start: 0.8909 (m-80) cc_final: 0.8696 (m-10)
REVERT: A  112 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8749 (tt0)
REVERT: A  113 PRO cc_start: 0.8735 (Cg_exo) cc_final: 0.8428 (Cg_endo)
REVERT: A  163 MET cc_start: 0.9534 (mtt) cc_final: 0.9319 (mtt)
REVERT: B   36 MET cc_start: 0.8629 (ptt) cc_final: 0.8405 (ptt)
REVERT: B  116 ASN cc_start: 0.9576 (t0) cc_final: 0.9103 (t0)
REVERT: B  132 CYS cc_start: 0.8844 (p) cc_final: 0.8628 (p)
REVERT: B  152 CYS cc_start: 0.8825 (t) cc_final: 0.8603 (t)
REVERT: B  189 ASN cc_start: 0.8993 (m-40) cc_final: 0.8374 (t0)
REVERT: B  204 GLN cc_start: 0.8487 (mt0) cc_final: 0.8113 (mm110)
REVERT: B  206 VAL cc_start: 0.8927 (m) cc_final: 0.8596 (p)
REVERT: B  315 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8150 (mtm110)
REVERT: B  321 ASP cc_start: 0.8930 (t0) cc_final: 0.8544 (t0)
REVERT: B  353 ASP cc_start: 0.8909 (t0) cc_final: 0.8398 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1519
  time to fit residues: 18.9720
Evaluate side-chains
  83 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.6634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4463  Z= 0.172
  Angle     :  0.569   8.485   6074  Z= 0.296
  Chirality :  0.045   0.146    673
  Planarity :  0.004   0.049    782
  Dihedral  :  4.399  16.369    594
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.36), residues: 550
  helix: -1.75 (0.65), residues: 53
  sheet:  0.74 (0.39), residues: 191
  loop : -0.90 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 170 
 HIS   0.002   0.001   HIS B 283 
 PHE   0.016   0.002   PHE B  62 
 TYR   0.009   0.001   TYR B 278 
 ARG   0.003   0.000   ARG B 147 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9113 (m100) cc_final: 0.8270 (m100)
REVERT: A   69 THR cc_start: 0.9124 (m) cc_final: 0.8782 (p)
REVERT: A   82 LYS cc_start: 0.8853 (mttt) cc_final: 0.8295 (mmmt)
REVERT: A  112 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8813 (tt0)
REVERT: A  113 PRO cc_start: 0.8706 (Cg_exo) cc_final: 0.8376 (Cg_endo)
REVERT: A  163 MET cc_start: 0.9506 (mtt) cc_final: 0.9243 (mtt)
REVERT: A  166 ASP cc_start: 0.8845 (t70) cc_final: 0.7967 (t70)
REVERT: B  110 GLN cc_start: 0.8577 (tt0) cc_final: 0.8294 (tm-30)
REVERT: B  116 ASN cc_start: 0.9480 (t0) cc_final: 0.9114 (t0)
REVERT: B  152 CYS cc_start: 0.8776 (t) cc_final: 0.8466 (t)
REVERT: B  189 ASN cc_start: 0.8946 (m-40) cc_final: 0.8331 (t0)
REVERT: B  204 GLN cc_start: 0.8563 (mt0) cc_final: 0.8169 (mm110)
REVERT: B  206 VAL cc_start: 0.8927 (m) cc_final: 0.8603 (p)
REVERT: B  279 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8792 (mm-30)
REVERT: B  321 ASP cc_start: 0.8880 (t0) cc_final: 0.8641 (t0)
REVERT: B  353 ASP cc_start: 0.8737 (t0) cc_final: 0.8353 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1194
  time to fit residues: 16.8662
Evaluate side-chains
  87 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 45 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.6729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4463  Z= 0.171
  Angle     :  0.557   5.943   6074  Z= 0.289
  Chirality :  0.045   0.158    673
  Planarity :  0.004   0.049    782
  Dihedral  :  4.224  16.597    594
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.36), residues: 550
  helix: -1.89 (0.64), residues: 53
  sheet:  0.67 (0.39), residues: 191
  loop : -0.84 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 170 
 HIS   0.002   0.000   HIS B 283 
 PHE   0.016   0.002   PHE B  62 
 TYR   0.008   0.001   TYR B 105 
 ARG   0.007   0.000   ARG B 315 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9101 (m100) cc_final: 0.8293 (m100)
REVERT: A   48 ASN cc_start: 0.8321 (t0) cc_final: 0.7710 (t0)
REVERT: A   69 THR cc_start: 0.9045 (m) cc_final: 0.8692 (p)
REVERT: A   82 LYS cc_start: 0.8854 (mttt) cc_final: 0.8302 (mmmt)
REVERT: A  112 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8873 (tt0)
REVERT: A  113 PRO cc_start: 0.8664 (Cg_exo) cc_final: 0.8381 (Cg_endo)
REVERT: A  122 PHE cc_start: 0.8946 (p90) cc_final: 0.8691 (p90)
REVERT: A  163 MET cc_start: 0.9508 (mtt) cc_final: 0.9258 (mtt)
REVERT: A  166 ASP cc_start: 0.8786 (t70) cc_final: 0.7909 (t70)
REVERT: B   46 TYR cc_start: 0.8727 (m-80) cc_final: 0.8435 (m-80)
REVERT: B  110 GLN cc_start: 0.8546 (tt0) cc_final: 0.8268 (tm-30)
REVERT: B  116 ASN cc_start: 0.9420 (t0) cc_final: 0.9134 (t0)
REVERT: B  152 CYS cc_start: 0.8799 (t) cc_final: 0.8154 (t)
REVERT: B  189 ASN cc_start: 0.8932 (m-40) cc_final: 0.8334 (t0)
REVERT: B  206 VAL cc_start: 0.8926 (m) cc_final: 0.8639 (p)
REVERT: B  321 ASP cc_start: 0.8849 (t0) cc_final: 0.8610 (t0)
REVERT: B  353 ASP cc_start: 0.8818 (t0) cc_final: 0.8388 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1121
  time to fit residues: 15.8436
Evaluate side-chains
  85 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 45 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.6982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4463  Z= 0.341
  Angle     :  0.640   7.873   6074  Z= 0.332
  Chirality :  0.047   0.159    673
  Planarity :  0.005   0.050    782
  Dihedral  :  4.484  16.472    594
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.36), residues: 550
  helix: -1.76 (0.66), residues: 53
  sheet:  0.53 (0.38), residues: 195
  loop : -0.91 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 115 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.019   0.002   PHE B 202 
 TYR   0.026   0.002   TYR B 278 
 ARG   0.006   0.001   ARG B 315 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A    8 SER cc_start: 0.7751 (t) cc_final: 0.7297 (m)
REVERT: A   47 TRP cc_start: 0.9159 (m100) cc_final: 0.8314 (m100)
REVERT: A   69 THR cc_start: 0.9108 (m) cc_final: 0.8756 (p)
REVERT: A   82 LYS cc_start: 0.8851 (mttt) cc_final: 0.8298 (mmmt)
REVERT: A  112 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8866 (tt0)
REVERT: A  113 PRO cc_start: 0.8692 (Cg_exo) cc_final: 0.8393 (Cg_endo)
REVERT: A  163 MET cc_start: 0.9552 (mtt) cc_final: 0.9313 (mtt)
REVERT: A  166 ASP cc_start: 0.9010 (t70) cc_final: 0.8148 (t70)
REVERT: B   36 MET cc_start: 0.8252 (tmm) cc_final: 0.7992 (tmm)
REVERT: B   43 LEU cc_start: 0.8666 (tp) cc_final: 0.8413 (tp)
REVERT: B  110 GLN cc_start: 0.8713 (tt0) cc_final: 0.8318 (tm-30)
REVERT: B  116 ASN cc_start: 0.9469 (t0) cc_final: 0.9208 (t0)
REVERT: B  186 ASP cc_start: 0.8937 (m-30) cc_final: 0.8653 (m-30)
REVERT: B  204 GLN cc_start: 0.8610 (mt0) cc_final: 0.8168 (mm110)
REVERT: B  206 VAL cc_start: 0.8991 (m) cc_final: 0.8658 (p)
REVERT: B  321 ASP cc_start: 0.8960 (t0) cc_final: 0.8651 (t0)
REVERT: B  353 ASP cc_start: 0.8803 (t0) cc_final: 0.8293 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1278
  time to fit residues: 17.0502
Evaluate side-chains
  87 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0270
   chunk 28 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.5244

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.105517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.092757 restraints weight = 6779.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.094223 restraints weight = 4824.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.095464 restraints weight = 3795.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.7098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4463  Z= 0.204
  Angle     :  0.597   9.738   6074  Z= 0.304
  Chirality :  0.045   0.160    673
  Planarity :  0.004   0.050    782
  Dihedral  :  4.294  18.967    594
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.36), residues: 550
  helix: -1.72 (0.68), residues: 51
  sheet:  0.59 (0.38), residues: 193
  loop : -0.89 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 115 
 HIS   0.002   0.000   HIS B 283 
 PHE   0.015   0.002   PHE B  62 
 TYR   0.008   0.001   TYR B 278 
 ARG   0.006   0.000   ARG B 315 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.12 seconds
wall clock time: 27 minutes 21.51 seconds (1641.51 seconds total)