Starting phenix.real_space_refine
on Tue Feb 13 18:34:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhr_29100/02_2024/8fhr_29100_updated.pdb"
  }
  resolution = 2.9
  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=   0.063
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: 7
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     Cl      2      4.86       5
     Na      2      4.78       5
     C    4836      2.51       5
     N    1144      2.21       5
     O    1268      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  214": "OE1" <-> "OE2"
    Residue "A ASP  255": "OD1" <-> "OD2"
    Residue "A ASP  366": "OD1" <-> "OD2"
    Residue "A ASP  407": "OD1" <-> "OD2"
    Residue "A TYR  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  485": "OE1" <-> "OE2"
    Residue "A PHE  519": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  582": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  214": "OE1" <-> "OE2"
    Residue "B ASP  366": "OD1" <-> "OD2"
    Residue "B ASP  407": "OD1" <-> "OD2"
    Residue "B TYR  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  485": "OE1" <-> "OE2"
    Residue "B PHE  519": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  582": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7306
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3627
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 19, 'TRANS': 455}
    Chain: "B"
      Number of atoms: 3627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3627
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 19, 'TRANS': 455}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 26
          Unusual residues: {' NA': 1, 'XZF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 26
          Unusual residues: {' NA': 1, 'XZF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.11, per 1000 atoms: 0.56
  Number of scatterers: 7306
  At special positions: 0
  Unit cell: (89.44, 104.06, 95.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      2     17.00
     S      48     16.00
     Na      2     11.00
     F       6      9.00
     O    1268      8.00
     N    1144      7.00
     C    4836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 436 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 416 " - pdb=" SG  CYS B 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 430 " - pdb=" SG  CYS B 436 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 2.56
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      66.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 154 through 157
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 167 through 195
      removed outlier: 3.731A  pdb=" N   THR A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR A 182 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN A 195 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 4.278A  pdb=" N   LEU A 206 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER A 210 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU A 211 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 249
      removed outlier: 3.540A  pdb=" N   GLY A 217 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY A 237 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 248 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 277
      removed outlier: 3.759A  pdb=" N   GLY A 264 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 305
      removed outlier: 3.848A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 322 through 328
    Processing helix  chain 'A' and resid 340 through 351
      Proline residue:  A 349  - end of helix
    Processing helix  chain 'A' and resid 367 through 393
      Proline residue:  A 372  - end of helix
    Processing helix  chain 'A' and resid 420 through 422
      No H-bonds generated for 'chain 'A' and resid 420 through 422'
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 454 through 483
      removed outlier: 4.333A  pdb=" N   LEU A 466 " --> pdb=" O   GLY A 463 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER A 467 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 476 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 477 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 478 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL A 479 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   PHE A 480 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLN A 481 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 522
      removed outlier: 4.080A  pdb=" N   LEU A 511 " --> pdb=" O   ARG A 507 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 552
      removed outlier: 3.586A  pdb=" N   PHE A 536 " --> pdb=" O   ILE A 532 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 537 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 539 " --> pdb=" O   PHE A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 584
      removed outlier: 3.657A  pdb=" N   VAL A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 604
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 154 through 157
      No H-bonds generated for 'chain 'B' and resid 154 through 157'
    Processing helix  chain 'B' and resid 159 through 165
    Processing helix  chain 'B' and resid 167 through 195
      removed outlier: 3.730A  pdb=" N   THR B 180 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN B 195 " --> pdb=" O   ALA B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 211
      removed outlier: 4.277A  pdb=" N   LEU B 206 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 210 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU B 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 249
      removed outlier: 3.539A  pdb=" N   GLY B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA B 228 " --> pdb=" O   ALA B 224 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU B 248 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 277
      removed outlier: 3.984A  pdb=" N   ARG B 261 " --> pdb=" O   ILE B 257 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLY B 264 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 305
      removed outlier: 3.848A  pdb=" N   LEU B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 322 through 328
    Processing helix  chain 'B' and resid 340 through 351
      Proline residue:  B 349  - end of helix
    Processing helix  chain 'B' and resid 367 through 393
      Proline residue:  B 372  - end of helix
    Processing helix  chain 'B' and resid 420 through 422
      No H-bonds generated for 'chain 'B' and resid 420 through 422'
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 446 through 450
    Processing helix  chain 'B' and resid 454 through 484
      removed outlier: 4.332A  pdb=" N   LEU B 466 " --> pdb=" O   GLY B 463 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER B 467 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 476 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA B 477 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS B 478 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL B 479 " --> pdb=" O   ALA B 476 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   PHE B 480 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLN B 481 " --> pdb=" O   LYS B 478 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   CYS B 484 " --> pdb=" O   GLN B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 522
      removed outlier: 4.079A  pdb=" N   LEU B 511 " --> pdb=" O   ARG B 507 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE B 522 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 552
      removed outlier: 3.587A  pdb=" N   PHE B 536 " --> pdb=" O   ILE B 532 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER B 539 " --> pdb=" O   PHE B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 584
      removed outlier: 3.656A  pdb=" N   VAL B 578 " --> pdb=" O   ALA B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 604

    406 hydrogen bonds defined for protein.
    1080 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: 1.95

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1099
        1.31 -     1.44: 2157
        1.44 -     1.56: 4172
        1.56 -     1.69: 4
        1.69 -     1.81: 72
  Bond restraints: 7504
  Sorted by residual:
  bond pdb=" C   ASN A 149 "
       pdb=" O   ASN A 149 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.29e-02 6.01e+03 1.41e+01
  bond pdb=" C   ASN B 149 "
       pdb=" O   ASN B 149 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.29e-02 6.01e+03 1.39e+01
  bond pdb=" CA  ASN B 149 "
       pdb=" C   ASN B 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.37e-02 5.33e+03 1.33e+01
  bond pdb=" CA  ASN A 149 "
       pdb=" C   ASN A 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.37e-02 5.33e+03 8.65e+00
  bond pdb=" C16 XZF B1101 "
       pdb=" C17 XZF B1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.315  0.053 2.00e-02 2.50e+03 6.99e+00
  ... (remaining 7499 not shown)

  Histogram of bond angle deviations from ideal:
       98.54 -   105.79: 137
      105.79 -   113.03: 4075
      113.03 -   120.27: 3046
      120.27 -   127.52: 2913
      127.52 -   134.76: 85
  Bond angle restraints: 10256
  Sorted by residual:
  angle pdb=" C   ASP A 255 "
        pdb=" N   PRO A 256 "
        pdb=" CA  PRO A 256 "
      ideal   model   delta    sigma   weight residual
     119.82  116.16    3.66 9.80e-01 1.04e+00 1.39e+01
  angle pdb=" C   ALA B 251 "
        pdb=" N   PRO B 252 "
        pdb=" CA  PRO B 252 "
      ideal   model   delta    sigma   weight residual
     119.84  115.19    4.65 1.25e+00 6.40e-01 1.39e+01
  angle pdb=" O   LEU A 148 "
        pdb=" C   LEU A 148 "
        pdb=" N   ASN A 149 "
      ideal   model   delta    sigma   weight residual
     122.27  117.88    4.39 1.23e+00 6.61e-01 1.27e+01
  angle pdb=" C   ILE B 257 "
        pdb=" CA  ILE B 257 "
        pdb=" CB  ILE B 257 "
      ideal   model   delta    sigma   weight residual
     111.88  107.59    4.29 1.28e+00 6.10e-01 1.12e+01
  angle pdb=" CA  LEU A 148 "
        pdb=" C   LEU A 148 "
        pdb=" N   ASN A 149 "
      ideal   model   delta    sigma   weight residual
     117.72  122.08   -4.36 1.31e+00 5.83e-01 1.11e+01
  ... (remaining 10251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 3870
       16.41 -    32.83: 308
       32.83 -    49.24: 68
       49.24 -    65.65: 16
       65.65 -    82.06: 8
  Dihedral angle restraints: 4270
    sinusoidal: 1560
      harmonic: 2710
  Sorted by residual:
  dihedral pdb=" CB  CYS A 416 "
           pdb=" SG  CYS A 416 "
           pdb=" SG  CYS A 421 "
           pdb=" CB  CYS A 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.06   82.06     1      1.00e+01 1.00e-02 8.27e+01
  dihedral pdb=" CB  CYS B 416 "
           pdb=" SG  CYS B 416 "
           pdb=" SG  CYS B 421 "
           pdb=" CB  CYS B 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.05   82.05     1      1.00e+01 1.00e-02 8.27e+01
  dihedral pdb=" CB  CYS B 430 "
           pdb=" SG  CYS B 430 "
           pdb=" SG  CYS B 436 "
           pdb=" CB  CYS B 436 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.56  -37.56     1      1.00e+01 1.00e-02 1.99e+01
  ... (remaining 4267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 694
       0.041 -    0.081: 379
       0.081 -    0.122: 103
       0.122 -    0.163: 13
       0.163 -    0.204: 3
  Chirality restraints: 1192
  Sorted by residual:
  chirality pdb=" CA  ASN A 149 "
            pdb=" N   ASN A 149 "
            pdb=" C   ASN A 149 "
            pdb=" CB  ASN A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  ARG A 399 "
            pdb=" N   ARG A 399 "
            pdb=" C   ARG A 399 "
            pdb=" CB  ARG A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  ARG B 399 "
            pdb=" N   ARG B 399 "
            pdb=" C   ARG B 399 "
            pdb=" CB  ARG B 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 1189 not shown)

  Planarity restraints: 1246
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 148 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" C   LEU A 148 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LEU A 148 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN A 149 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 330 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.51e+00
        pdb=" N   PRO B 331 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 331 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 331 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 330 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.50e+00
        pdb=" N   PRO A 331 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1243 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2141
        2.81 -     3.33: 6978
        3.33 -     3.86: 11761
        3.86 -     4.38: 14041
        4.38 -     4.90: 24275
  Nonbonded interactions: 59196
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 148 "
            pdb="NA    NA B1102 "
     model   vdw
     2.289 2.470
  nonbonded pdb=" O   LEU A 148 "
            pdb="NA    NA A1102 "
     model   vdw
     2.289 2.470
  nonbonded pdb=" OG  SER B 468 "
            pdb="NA    NA B1102 "
     model   vdw
     2.304 2.470
  nonbonded pdb=" O   ALA A 464 "
            pdb="NA    NA A1102 "
     model   vdw
     2.304 2.470
  nonbonded pdb=" OG  SER A 468 "
            pdb="NA    NA A1102 "
     model   vdw
     2.304 2.470
  ... (remaining 59191 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.340
  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:          7.200
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     22.060
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  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:12.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
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      :  0.009   0.053   7504  Z= 0.553
  Angle     :  0.819   9.762  10256  Z= 0.439
  Chirality :  0.049   0.204   1192
  Planarity :  0.005   0.047   1246
  Dihedral  : 13.154  76.398   2534
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  1.96 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.64 (0.25), residues: 946
  helix: -0.34 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.57 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 161 
 HIS   0.003   0.002   HIS B 549 
 PHE   0.032   0.003   PHE A 318 
 TYR   0.028   0.002   TYR A 443 
 ARG   0.004   0.001   ARG A 507 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  400 ASP cc_start: 0.8726 (m-30) cc_final: 0.8483 (m-30)
REVERT: A  407 ASP cc_start: 0.8171 (m-30) cc_final: 0.7960 (m-30)
REVERT: A  434 HIS cc_start: 0.6564 (m-70) cc_final: 0.6095 (m-70)
REVERT: A  447 MET cc_start: 0.8638 (ttt) cc_final: 0.8410 (ttm)
  outliers start: 5
  outliers final: 3
  residues processed: 95
  average time/residue: 0.8969
  time to fit residues: 91.9763
Evaluate side-chains
  78 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.0670
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
A 359 ASN
A 481 GLN
A 526 ASN
B 359 ASN
B 481 GLN
B 526 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7504  Z= 0.156
  Angle     :  0.499   7.294  10256  Z= 0.258
  Chirality :  0.038   0.151   1192
  Planarity :  0.004   0.042   1246
  Dihedral  :  6.111  58.034   1030
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  5.87 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.37 (0.27), residues: 946
  helix:  0.76 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.27 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 425 
 HIS   0.003   0.001   HIS A 234 
 PHE   0.008   0.001   PHE B 223 
 TYR   0.009   0.001   TYR B 443 
 ARG   0.003   0.000   ARG A 209 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A  399 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8091 (mtt-85)
REVERT: A  400 ASP cc_start: 0.8626 (m-30) cc_final: 0.8376 (m-30)
REVERT: A  447 MET cc_start: 0.8555 (ttt) cc_final: 0.8330 (ttm)
REVERT: B  400 ASP cc_start: 0.8676 (m-30) cc_final: 0.8457 (m-30)
  outliers start: 11
  outliers final: 4
  residues processed: 96
  average time/residue: 0.9052
  time to fit residues: 94.1059
Evaluate side-chains
  82 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  527 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A 526 ASN
B 299 ASN
B 526 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7504  Z= 0.167
  Angle     :  0.483   5.950  10256  Z= 0.245
  Chirality :  0.038   0.149   1192
  Planarity :  0.004   0.037   1246
  Dihedral  :  5.734  55.828   1030
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.44 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.05 (0.27), residues: 946
  helix:  0.95 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.06 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 568 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.010   0.001   PHE A 545 
 TYR   0.008   0.001   TYR A 443 
 ARG   0.003   0.000   ARG A 209 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  400 ASP cc_start: 0.8602 (m-30) cc_final: 0.8378 (m-30)
REVERT: B  400 ASP cc_start: 0.8658 (m-30) cc_final: 0.8392 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 79
  average time/residue: 0.8579
  time to fit residues: 73.6010
Evaluate side-chains
  73 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
B 526 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7504  Z= 0.206
  Angle     :  0.498   5.723  10256  Z= 0.251
  Chirality :  0.039   0.148   1192
  Planarity :  0.004   0.035   1246
  Dihedral  :  5.611  53.791   1030
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.23 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.05 (0.27), residues: 946
  helix:  1.02 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.01 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.002   0.001   HIS B 549 
 PHE   0.011   0.001   PHE A 545 
 TYR   0.008   0.001   TYR B 443 
 ARG   0.001   0.000   ARG B 399 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.781 
Fit side-chains
  outliers start: 13
  outliers final: 6
  residues processed: 77
  average time/residue: 0.8973
  time to fit residues: 74.6864
Evaluate side-chains
  73 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 67 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A 526 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7504  Z= 0.201
  Angle     :  0.490   5.303  10256  Z= 0.247
  Chirality :  0.039   0.150   1192
  Planarity :  0.004   0.033   1246
  Dihedral  :  5.309  52.923   1028
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.88 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.17 (0.27), residues: 946
  helix:  1.11 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.95 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS B 549 
 PHE   0.011   0.001   PHE A 545 
 TYR   0.007   0.001   TYR A 443 
 ARG   0.002   0.000   ARG A 321 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  400 ASP cc_start: 0.8538 (m-30) cc_final: 0.8266 (m-30)
REVERT: B  524 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7151 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 77
  average time/residue: 0.9802
  time to fit residues: 81.1257
Evaluate side-chains
  79 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0050
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 87 optimal weight:    0.3980
   overall best weight:    0.7996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7504  Z= 0.173
  Angle     :  0.465   5.269  10256  Z= 0.236
  Chirality :  0.038   0.179   1192
  Planarity :  0.003   0.032   1246
  Dihedral  :  5.130  52.167   1028
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.66 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.36 (0.27), residues: 946
  helix:  1.27 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.90 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 549 
 PHE   0.009   0.001   PHE A 545 
 TYR   0.006   0.001   TYR A 443 
 ARG   0.001   0.000   ARG B 399 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: A  400 ASP cc_start: 0.8518 (m-30) cc_final: 0.8238 (m-30)
  outliers start: 18
  outliers final: 10
  residues processed: 80
  average time/residue: 0.9036
  time to fit residues: 78.1236
Evaluate side-chains
  77 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A 526 ASN
B 299 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7504  Z= 0.180
  Angle     :  0.469   5.284  10256  Z= 0.238
  Chirality :  0.038   0.153   1192
  Planarity :  0.003   0.031   1246
  Dihedral  :  4.901  50.998   1026
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.79 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.48 (0.27), residues: 946
  helix:  1.34 (0.21), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.82 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 568 
 HIS   0.002   0.001   HIS A 549 
 PHE   0.012   0.001   PHE A 598 
 TYR   0.006   0.001   TYR A 443 
 ARG   0.001   0.000   ARG B 399 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7610 (tm130)
REVERT: A  400 ASP cc_start: 0.8529 (m-30) cc_final: 0.8244 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 77
  average time/residue: 1.0586
  time to fit residues: 87.4042
Evaluate side-chains
  79 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  327 GLN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  437 HIS
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 86 optimal weight:    0.4980
   chunk 79 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7504  Z= 0.171
  Angle     :  0.464   6.426  10256  Z= 0.234
  Chirality :  0.038   0.152   1192
  Planarity :  0.003   0.031   1246
  Dihedral  :  4.790  50.311   1026
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.71 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.27), residues: 946
  helix:  1.40 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.71 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS B 549 
 PHE   0.009   0.001   PHE A 545 
 TYR   0.006   0.001   TYR A 443 
 ARG   0.002   0.000   ARG B 209 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7717 (tm130)
REVERT: A  400 ASP cc_start: 0.8531 (m-30) cc_final: 0.8221 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 72
  average time/residue: 1.0242
  time to fit residues: 79.4852
Evaluate side-chains
  74 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  327 GLN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  437 HIS
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  399 ARG
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0070
   chunk 25 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0370
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7504  Z= 0.131
  Angle     :  0.430   5.648  10256  Z= 0.218
  Chirality :  0.037   0.155   1192
  Planarity :  0.003   0.031   1246
  Dihedral  :  4.470  47.328   1026
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.36 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.87 (0.28), residues: 946
  helix:  1.60 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.61 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 549 
 PHE   0.007   0.001   PHE B 223 
 TYR   0.005   0.001   TYR A 499 
 ARG   0.001   0.000   ARG B 209 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A  327 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (tm130)
REVERT: A  400 ASP cc_start: 0.8481 (m-30) cc_final: 0.8163 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 73
  average time/residue: 0.9952
  time to fit residues: 78.0431
Evaluate side-chains
  71 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  327 GLN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  437 HIS
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0670
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B 299 ASN
B 526 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   7504  Z= 0.143
  Angle     :  0.437   5.780  10256  Z= 0.221
  Chirality :  0.037   0.148   1192
  Planarity :  0.003   0.030   1246
  Dihedral  :  4.390  45.881   1026
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.88 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.99 (0.28), residues: 946
  helix:  1.67 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.52 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 549 
 PHE   0.008   0.001   PHE A 545 
 TYR   0.005   0.001   TYR A 443 
 ARG   0.001   0.000   ARG B 209 

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  327 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7655 (tm130)
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.9668
  time to fit residues: 74.0032
Evaluate side-chains
  72 residues out of total 766 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  327 GLN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  551 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
B 526 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.142037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.100788 restraints weight = 7944.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.96
r_work: 0.2986 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7504  Z= 0.198
  Angle     :  0.478   6.054  10256  Z= 0.241
  Chirality :  0.039   0.144   1192
  Planarity :  0.003   0.029   1246
  Dihedral  :  4.601  46.969   1026
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 15.27 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.77 (0.28), residues: 946
  helix:  1.43 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.54 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 161 
 HIS   0.002   0.001   HIS B 549 
 PHE   0.010   0.001   PHE B 545 
 TYR   0.007   0.001   TYR A 443 
 ARG   0.001   0.000   ARG B 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2324.27 seconds
wall clock time: 42 minutes 53.01 seconds (2573.01 seconds total)