Starting phenix.real_space_refine
on Fri Oct 10 18:36:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zl2_60216/10_2025/8zl2_60216.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      91      5.16       5
     C    5675      2.51       5
     N    1346      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 4206
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 33, 'TRANS': 508}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 4190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4190
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 33, 'TRANS': 505}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 92
          Unusual residues: {'4DS': 1, 'NAG': 1, 'PTY': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'NAG': 1, 'PTY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.32, per 1000 atoms: 0.27
  Number of scatterers: 8552
  At special positions: 0
  Unit cell: (90.2312, 103, 115.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      91     16.00
     P       2     15.00
     O    1438      8.00
     N    1346      7.00
     C    5675      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 352.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      81.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 40
      removed outlier: 3.720A  pdb=" N   PHE A  37 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 54
      removed outlier: 3.587A  pdb=" N   LEU A  44 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 54 through 60
      removed outlier: 3.842A  pdb=" N   ASN A  60 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 81
      removed outlier: 3.823A  pdb=" N   ARG A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 89
    Processing helix  chain 'A' and resid 90 through 100
      removed outlier: 4.237A  pdb=" N   VAL A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.582A  pdb=" N   TYR A 111 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 132
      removed outlier: 3.962A  pdb=" N   CYS A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 147
    Processing helix  chain 'A' and resid 149 through 166
    Processing helix  chain 'A' and resid 169 through 191
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 220 through 239
      removed outlier: 4.026A  pdb=" N   CYS A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 259
      removed outlier: 3.717A  pdb=" N   LEU A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 296
      Proline residue:  A 277  - end of helix
      removed outlier: 3.622A  pdb=" N   GLY A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.687A  pdb=" N   GLN A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
      removed outlier: 4.034A  pdb=" N   LYS A 320 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 353
      removed outlier: 3.873A  pdb=" N   ARG A 353 " --> pdb=" O   MET A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 365
      removed outlier: 3.761A  pdb=" N   LEU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 365 " --> pdb=" O   TRP A 361 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 365'
    Processing helix  chain 'A' and resid 372 through 386
      removed outlier: 4.008A  pdb=" N   THR A 376 " --> pdb=" O   ASN A 372 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 396
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 424 through 443
      removed outlier: 4.035A  pdb=" N   GLY A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 453
      removed outlier: 3.844A  pdb=" N   ILE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 458
      removed outlier: 4.321A  pdb=" N   VAL A 457 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 477
      removed outlier: 4.321A  pdb=" N   PHE A 477 " --> pdb=" O   PHE A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 499
      Proline residue:  A 489  - end of helix
    Processing helix  chain 'A' and resid 501 through 513
      removed outlier: 4.157A  pdb=" N   LEU A 505 " --> pdb=" O   HIS A 501 " (cutoff:3.500A)
      Proline residue:  A 508  - end of helix
    Processing helix  chain 'A' and resid 523 through 533
    Processing helix  chain 'A' and resid 536 through 544
      removed outlier: 3.604A  pdb=" N   MET A 540 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 567
      removed outlier: 3.611A  pdb=" N   THR A 548 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LEU A 564 " --> pdb=" O   GLN A 560 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 584
      removed outlier: 3.573A  pdb=" N   GLN A 578 " --> pdb=" O   PRO A 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 40
      removed outlier: 3.610A  pdb=" N   PHE B  37 " --> pdb=" O   CYS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 60
      removed outlier: 3.512A  pdb=" N   LEU B  44 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
      Proline residue:  B  55  - end of helix
      removed outlier: 3.873A  pdb=" N   ASN B  60 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 81
      removed outlier: 3.908A  pdb=" N   ARG B  66 " --> pdb=" O   GLY B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 89
    Processing helix  chain 'B' and resid 90 through 99
      removed outlier: 4.150A  pdb=" N   VAL B  94 " --> pdb=" O   MET B  90 " (cutoff:3.500A)
      Proline residue:  B  97  - end of helix
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.741A  pdb=" N   TYR B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 131
    Processing helix  chain 'B' and resid 133 through 146
      removed outlier: 4.002A  pdb=" N   ARG B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 166
    Processing helix  chain 'B' and resid 169 through 192
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 220 through 238
    Processing helix  chain 'B' and resid 239 through 244
      removed outlier: 5.960A  pdb=" N   ILE B 242 " --> pdb=" O   CYS B 239 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   ILE B 243 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 259
      removed outlier: 3.877A  pdb=" N   LEU B 249 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 296
      Proline residue:  B 277  - end of helix
    Processing helix  chain 'B' and resid 304 through 314
      removed outlier: 3.803A  pdb=" N   VAL B 308 " --> pdb=" O   GLU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 327
    Processing helix  chain 'B' and resid 333 through 352
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.603A  pdb=" N   ILE B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 384 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 395
      removed outlier: 3.589A  pdb=" N   LEU B 393 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 421
    Processing helix  chain 'B' and resid 423 through 443
      removed outlier: 4.533A  pdb=" N   PHE B 427 " --> pdb=" O   TRP B 423 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY B 443 " --> pdb=" O   SER B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 452
      removed outlier: 3.886A  pdb=" N   LEU B 447 " --> pdb=" O   GLY B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 458
      removed outlier: 3.708A  pdb=" N   VAL B 457 " --> pdb=" O   GLY B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 476
    Processing helix  chain 'B' and resid 479 through 498
      Proline residue:  B 489  - end of helix
    Processing helix  chain 'B' and resid 501 through 513
      removed outlier: 3.942A  pdb=" N   LEU B 505 " --> pdb=" O   HIS B 501 " (cutoff:3.500A)
      Proline residue:  B 508  - end of helix
    Processing helix  chain 'B' and resid 523 through 534
    Processing helix  chain 'B' and resid 536 through 544
      removed outlier: 3.557A  pdb=" N   MET B 540 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 567
      removed outlier: 3.527A  pdb=" N   THR B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLN B 560 " --> pdb=" O   PHE B 556 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   LEU B 564 " --> pdb=" O   GLN B 560 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL B 565 " --> pdb=" O   THR B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 584

    552 hydrogen bonds defined for protein.
    1626 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: 1.44

  Time building geometry restraints manager: 1.25 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: 1314
        1.32 -     1.44: 2306
        1.44 -     1.57: 5002
        1.57 -     1.69: 6
        1.69 -     1.81: 147
  Bond restraints: 8775
  Sorted by residual:
  bond pdb=" CAT 4DS A 601 "
       pdb=" NAS 4DS A 601 "
    ideal  model  delta    sigma   weight residual
    1.170  1.315 -0.145 2.00e-02 2.50e+03 5.28e+01
  bond pdb=" CBA 4DS A 601 "
       pdb=" NAZ 4DS A 601 "
    ideal  model  delta    sigma   weight residual
    1.170  1.313 -0.143 2.00e-02 2.50e+03 5.14e+01
  bond pdb=" N   VAL A 146 "
       pdb=" CA  VAL A 146 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.038 1.21e-02 6.83e+03 9.62e+00
  bond pdb=" N   VAL B 457 "
       pdb=" CA  VAL B 457 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.24e+00
  bond pdb=" N   VAL A 142 "
       pdb=" CA  VAL A 142 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.19e+00
  ... (remaining 8770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.84: 11926
       10.84 -    21.69: 0
       21.69 -    32.53: 0
       32.53 -    43.38: 0
       43.38 -    54.22: 2
  Bond angle restraints: 11928
  Sorted by residual:
  angle pdb=" CAP 4DS A 601 "
        pdb=" NAS 4DS A 601 "
        pdb=" CAT 4DS A 601 "
      ideal   model   delta    sigma   weight residual
     180.00  125.78   54.22 3.00e+00 1.11e-01 3.27e+02
  angle pdb=" CAG 4DS A 601 "
        pdb=" NAZ 4DS A 601 "
        pdb=" CBA 4DS A 601 "
      ideal   model   delta    sigma   weight residual
     177.62  124.15   53.47 3.00e+00 1.11e-01 3.18e+02
  angle pdb=" N   GLU B 304 "
        pdb=" CA  GLU B 304 "
        pdb=" C   GLU B 304 "
      ideal   model   delta    sigma   weight residual
     114.04  107.10    6.94 1.24e+00 6.50e-01 3.13e+01
  angle pdb=" CA  TYR A 282 "
        pdb=" CB  TYR A 282 "
        pdb=" CG  TYR A 282 "
      ideal   model   delta    sigma   weight residual
     113.90  122.67   -8.77 1.80e+00 3.09e-01 2.37e+01
  angle pdb=" N   LYS B 303 "
        pdb=" CA  LYS B 303 "
        pdb=" C   LYS B 303 "
      ideal   model   delta    sigma   weight residual
     113.56  107.00    6.56 1.39e+00 5.18e-01 2.23e+01
  ... (remaining 11923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.82: 5047
       24.82 -    49.63: 149
       49.63 -    74.45: 21
       74.45 -    99.27: 3
       99.27 -   124.09: 2
  Dihedral angle restraints: 5222
    sinusoidal: 2089
      harmonic: 3133
  Sorted by residual:
  dihedral pdb=" CA  PHE B  47 "
           pdb=" C   PHE B  47 "
           pdb=" N   LEU B  48 "
           pdb=" CA  LEU B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.62  -21.38     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" C3  PTY B 601 "
           pdb=" O11 PTY B 601 "
           pdb=" P1  PTY B 601 "
           pdb=" O12 PTY B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.23  176.14  124.09     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" N1  PTY B 601 "
           pdb=" C2  PTY B 601 "
           pdb=" C3  PTY B 601 "
           pdb=" O11 PTY B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33 -177.99 -116.68     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 5219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 950
       0.043 -    0.085: 312
       0.085 -    0.128: 102
       0.128 -    0.171: 18
       0.171 -    0.213: 5
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" CA  MET B 444 "
            pdb=" N   MET B 444 "
            pdb=" C   MET B 444 "
            pdb=" CB  MET B 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  TYR B 282 "
            pdb=" N   TYR B 282 "
            pdb=" C   TYR B 282 "
            pdb=" CB  TYR B 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CA  GLU B 304 "
            pdb=" N   GLU B 304 "
            pdb=" C   GLU B 304 "
            pdb=" CB  GLU B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.47e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 421 "    0.048 5.00e-02 4.00e+02   7.39e-02 8.75e+00
        pdb=" N   PRO B 422 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO B 422 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 422 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 546 "    0.047 5.00e-02 4.00e+02   7.20e-02 8.29e+00
        pdb=" N   PRO A 547 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 547 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 547 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 559 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.56e+00
        pdb=" C   CYS A 559 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   CYS A 559 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN A 560 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 982
        2.74 -     3.28: 8434
        3.28 -     3.82: 13197
        3.82 -     4.36: 15262
        4.36 -     4.90: 27313
  Nonbonded interactions: 65188
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 260 "
            pdb=" OH  TYR A 580 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ALA B 492 "
            pdb=" OG  SER B 495 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   PRO A 404 "
            pdb=" OG1 THR A 405 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" O   MET B 279 "
            pdb=" OG1 THR B 283 "
     model   vdw
     2.419 3.040
  nonbonded pdb=" O   ILE B  76 "
            pdb=" OG1 THR B  80 "
     model   vdw
     2.474 3.040
  ... (remaining 65183 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 32 through 147 or (resid 148 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 149 through 200 or (resid 215 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 216 through 584))
  selection = (chain 'B' and (resid 32 through 298 or (resid 299 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 300 through 302 or (resid 303 through 305 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 306 through 584 \ 
))
}

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:             1.300
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.340
  Find NCS groups from input model:        0.320
  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:9.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.145   8775  Z= 0.349
  Angle     :  1.051  54.224  11928  Z= 0.519
  Chirality :  0.048   0.213   1387
  Planarity :  0.006   0.074   1452
  Dihedral  : 12.491 124.086   3204
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.25), residues: 1073
  helix:  1.59 (0.18), residues: 787
  sheet:  None (None), residues: 0
  loop : -1.40 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 371 
 TYR   0.032   0.002   TYR A 282 
 PHE   0.024   0.002   PHE A 251 
 TRP   0.031   0.003   TRP B  78 
 HIS   0.017   0.002   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00730 ( 8775)
  covalent geometry    : angle       1.05082 (11928)
  hydrogen bonds       : bond        0.16345 (  552)
  hydrogen bonds       : angle       5.24821 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 MET cc_start: 0.8809 (mmt) cc_final: 0.8455 (mmm)
  outliers start: 0
  outliers final: 1
  residues processed: 104
  average time/residue: 0.6392
  time to fit residues: 70.7601
Evaluate side-chains
  80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 291 GLN
** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.069472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.051327 restraints weight = 21946.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.02
r_work: 0.2625 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8775  Z= 0.131
  Angle     :  0.560   7.515  11928  Z= 0.303
  Chirality :  0.040   0.163   1387
  Planarity :  0.005   0.063   1452
  Dihedral  :  8.641 126.533   1285
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  5.29 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.25), residues: 1073
  helix:  1.99 (0.18), residues: 789
  sheet:  None (None), residues: 0
  loop : -1.23 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.024   0.001   TYR B 282 
 PHE   0.028   0.001   PHE A 251 
 TRP   0.013   0.001   TRP B 562 
 HIS   0.010   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8775)
  covalent geometry    : angle       0.55968 (11928)
  hydrogen bonds       : bond        0.05005 (  552)
  hydrogen bonds       : angle       4.03803 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8505 (mtm)
REVERT: A  316 ASP cc_start: 0.8977 (t0) cc_final: 0.8448 (p0)
REVERT: A  328 ASP cc_start: 0.8825 (m-30) cc_final: 0.8487 (m-30)
REVERT: B  260 LYS cc_start: 0.9275 (tttt) cc_final: 0.9061 (mttp)
REVERT: B  295 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7753 (mtt)
  outliers start: 8
  outliers final: 0
  residues processed: 88
  average time/residue: 0.6192
  time to fit residues: 58.0565
Evaluate side-chains
  77 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain B residue  295 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 90 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.068275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.050158 restraints weight = 21926.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2726 rms_B_bonded: 2.99
r_work: 0.2598 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8775  Z= 0.129
  Angle     :  0.524   6.906  11928  Z= 0.281
  Chirality :  0.039   0.170   1387
  Planarity :  0.005   0.061   1452
  Dihedral  :  7.056  58.176   1282
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.49 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.25), residues: 1073
  helix:  2.23 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop : -1.06 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 109 
 TYR   0.025   0.001   TYR B 282 
 PHE   0.024   0.001   PHE A 251 
 TRP   0.011   0.001   TRP B 414 
 HIS   0.010   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8775)
  covalent geometry    : angle       0.52430 (11928)
  hydrogen bonds       : bond        0.04962 (  552)
  hydrogen bonds       : angle       3.92110 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 ASP cc_start: 0.8855 (m-30) cc_final: 0.8336 (m-30)
REVERT: B  260 LYS cc_start: 0.9324 (tttt) cc_final: 0.9103 (mttp)
REVERT: B  295 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7478 (mtt)
REVERT: B  370 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7851 (mp)
  outliers start: 10
  outliers final: 1
  residues processed: 83
  average time/residue: 0.6238
  time to fit residues: 55.1320
Evaluate side-chains
  78 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 101 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 53 optimal weight:    0.2980
   chunk 11 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.064230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.046151 restraints weight = 22827.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2621 rms_B_bonded: 3.01
r_work: 0.2485 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8775  Z= 0.218
  Angle     :  0.609   9.878  11928  Z= 0.325
  Chirality :  0.042   0.187   1387
  Planarity :  0.005   0.058   1452
  Dihedral  :  7.210  58.643   1282
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.58 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.26), residues: 1073
  helix:  2.22 (0.19), residues: 779
  sheet:  None (None), residues: 0
  loop : -1.12 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 109 
 TYR   0.024   0.002   TYR A 282 
 PHE   0.024   0.002   PHE A 251 
 TRP   0.013   0.001   TRP B 414 
 HIS   0.013   0.002   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 8775)
  covalent geometry    : angle       0.60903 (11928)
  hydrogen bonds       : bond        0.06450 (  552)
  hydrogen bonds       : angle       4.15061 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 ASP cc_start: 0.8902 (m-30) cc_final: 0.8525 (m-30)
REVERT: B  260 LYS cc_start: 0.9465 (tttt) cc_final: 0.9199 (ttmm)
  outliers start: 7
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6317
  time to fit residues: 52.4964
Evaluate side-chains
  78 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain B residue  145 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.067227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.049049 restraints weight = 22365.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.2712 rms_B_bonded: 3.01
r_work: 0.2582 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8775  Z= 0.126
  Angle     :  0.519   7.997  11928  Z= 0.277
  Chirality :  0.039   0.165   1387
  Planarity :  0.005   0.057   1452
  Dihedral  :  6.892  58.912   1282
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.13 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1073
  helix:  2.27 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.06 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 109 
 TYR   0.023   0.001   TYR B 282 
 PHE   0.020   0.001   PHE A 251 
 TRP   0.011   0.001   TRP A 562 
 HIS   0.010   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8775)
  covalent geometry    : angle       0.51860 (11928)
  hydrogen bonds       : bond        0.04740 (  552)
  hydrogen bonds       : angle       3.89878 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8942 (m-30) cc_final: 0.8529 (m-30)
REVERT: A  515 MET cc_start: 0.8975 (mmt) cc_final: 0.8689 (mmt)
REVERT: B  260 LYS cc_start: 0.9411 (tttt) cc_final: 0.9156 (ttmm)
REVERT: B  295 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7450 (mtt)
REVERT: B  370 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8017 (mp)
  outliers start: 16
  outliers final: 4
  residues processed: 85
  average time/residue: 0.6043
  time to fit residues: 54.8336
Evaluate side-chains
  81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.2980
   chunk 68 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.069214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.051150 restraints weight = 22168.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 3.02
r_work: 0.2630 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8775  Z= 0.108
  Angle     :  0.501   9.773  11928  Z= 0.263
  Chirality :  0.038   0.157   1387
  Planarity :  0.005   0.059   1452
  Dihedral  :  6.589  58.786   1282
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.45 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.26), residues: 1073
  helix:  2.34 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.98 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 109 
 TYR   0.024   0.001   TYR B 282 
 PHE   0.019   0.001   PHE A 268 
 TRP   0.009   0.001   TRP B 414 
 HIS   0.008   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8775)
  covalent geometry    : angle       0.50057 (11928)
  hydrogen bonds       : bond        0.04030 (  552)
  hydrogen bonds       : angle       3.76414 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8918 (m-30) cc_final: 0.8354 (m-30)
REVERT: B  295 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7240 (mtt)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.5992
  time to fit residues: 49.9931
Evaluate side-chains
  82 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  523 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0470
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.0240

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.068894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.050812 restraints weight = 22487.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.2754 rms_B_bonded: 3.04
r_work: 0.2627 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8775  Z= 0.112
  Angle     :  0.505  10.445  11928  Z= 0.264
  Chirality :  0.038   0.159   1387
  Planarity :  0.005   0.057   1452
  Dihedral  :  6.480  57.526   1282
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.34 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.26), residues: 1073
  helix:  2.38 (0.18), residues: 779
  sheet:  None (None), residues: 0
  loop : -0.91 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 109 
 TYR   0.023   0.001   TYR B 282 
 PHE   0.020   0.001   PHE A 268 
 TRP   0.009   0.001   TRP B 414 
 HIS   0.008   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8775)
  covalent geometry    : angle       0.50491 (11928)
  hydrogen bonds       : bond        0.04139 (  552)
  hydrogen bonds       : angle       3.73304 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8920 (m-30) cc_final: 0.8367 (m-30)
REVERT: B  260 LYS cc_start: 0.9404 (tttt) cc_final: 0.9147 (ttmm)
REVERT: B  295 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7271 (mtt)
  outliers start: 12
  outliers final: 4
  residues processed: 82
  average time/residue: 0.5992
  time to fit residues: 52.4961
Evaluate side-chains
  80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 MET
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  523 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 6 optimal weight:    0.2980
   chunk 59 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0970
   chunk 28 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0070
   chunk 45 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.071252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.053240 restraints weight = 22303.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 3.04
r_work: 0.2672 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8775  Z= 0.103
  Angle     :  0.492  10.562  11928  Z= 0.255
  Chirality :  0.037   0.147   1387
  Planarity :  0.005   0.058   1452
  Dihedral  :  6.318  56.406   1282
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.44 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.26), residues: 1073
  helix:  2.38 (0.18), residues: 779
  sheet:  None (None), residues: 0
  loop : -0.88 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 152 
 TYR   0.024   0.001   TYR B 282 
 PHE   0.023   0.001   PHE A 268 
 TRP   0.009   0.001   TRP A 562 
 HIS   0.006   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8775)
  covalent geometry    : angle       0.49150 (11928)
  hydrogen bonds       : bond        0.03516 (  552)
  hydrogen bonds       : angle       3.64864 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8895 (m-30) cc_final: 0.8355 (m-30)
REVERT: B  176 MET cc_start: 0.8697 (ttm) cc_final: 0.8408 (mtp)
REVERT: B  295 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7006 (mtt)
REVERT: B  316 ASP cc_start: 0.8673 (p0) cc_final: 0.8469 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 81
  average time/residue: 0.6110
  time to fit residues: 52.8748
Evaluate side-chains
  82 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  523 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 102 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.069749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.051389 restraints weight = 22329.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2767 rms_B_bonded: 3.06
r_work: 0.2640 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8775  Z= 0.113
  Angle     :  0.520  12.265  11928  Z= 0.265
  Chirality :  0.038   0.156   1387
  Planarity :  0.005   0.058   1452
  Dihedral  :  6.291  55.812   1282
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 13.22 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.26), residues: 1073
  helix:  2.42 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.85 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 109 
 TYR   0.024   0.001   TYR B 282 
 PHE   0.019   0.001   PHE A 268 
 TRP   0.009   0.001   TRP A 562 
 HIS   0.007   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8775)
  covalent geometry    : angle       0.51958 (11928)
  hydrogen bonds       : bond        0.03961 (  552)
  hydrogen bonds       : angle       3.66165 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8885 (m-30) cc_final: 0.8337 (m-30)
REVERT: B  176 MET cc_start: 0.8659 (ttm) cc_final: 0.8394 (mtp)
REVERT: B  260 LYS cc_start: 0.9398 (tttt) cc_final: 0.9136 (ttmm)
REVERT: B  295 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7062 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.6632
  time to fit residues: 56.4667
Evaluate side-chains
  80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  523 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.065598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.047513 restraints weight = 22540.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 3.01
r_work: 0.2529 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8775  Z= 0.182
  Angle     :  0.599  13.176  11928  Z= 0.309
  Chirality :  0.040   0.180   1387
  Planarity :  0.005   0.056   1452
  Dihedral  :  6.589  57.137   1282
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 13.22 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.26), residues: 1073
  helix:  2.40 (0.19), residues: 779
  sheet:  None (None), residues: 0
  loop : -0.92 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 109 
 TYR   0.027   0.001   TYR A 282 
 PHE   0.023   0.001   PHE A 251 
 TRP   0.010   0.001   TRP B 414 
 HIS   0.011   0.002   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8775)
  covalent geometry    : angle       0.59867 (11928)
  hydrogen bonds       : bond        0.05519 (  552)
  hydrogen bonds       : angle       3.89013 ( 1626)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.8928 (m-30) cc_final: 0.8413 (m-30)
REVERT: B  195 LYS cc_start: 0.9049 (mttp) cc_final: 0.8797 (mppt)
REVERT: B  260 LYS cc_start: 0.9469 (tttt) cc_final: 0.9214 (ttmm)
REVERT: B  404 PRO cc_start: 0.9575 (Cg_exo) cc_final: 0.9325 (Cg_endo)
  outliers start: 3
  outliers final: 4
  residues processed: 80
  average time/residue: 0.6572
  time to fit residues: 55.9556
Evaluate side-chains
  80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain B residue  145 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0010
   overall best weight:    0.7994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.067797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.049218 restraints weight = 22408.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 3.07
r_work: 0.2589 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8775  Z= 0.121
  Angle     :  0.560  13.080  11928  Z= 0.287
  Chirality :  0.038   0.162   1387
  Planarity :  0.005   0.058   1452
  Dihedral  :  6.503  56.363   1282
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 13.66 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.26), residues: 1073
  helix:  2.40 (0.18), residues: 777
  sheet:  None (None), residues: 0
  loop : -0.88 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 109 
 TYR   0.028   0.001   TYR A 282 
 PHE   0.019   0.001   PHE A 268 
 TRP   0.011   0.001   TRP B 414 
 HIS   0.009   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8775)
  covalent geometry    : angle       0.55965 (11928)
  hydrogen bonds       : bond        0.04560 (  552)
  hydrogen bonds       : angle       3.76044 ( 1626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2321.94 seconds
wall clock time: 40 minutes 25.04 seconds (2425.04 seconds total)