Starting phenix.real_space_refine
on Mon Jan 13 23:50:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rfb_19117/01_2025/8rfb_19117_neut.cif"
  }
  resolution = 4.01
  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=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    2979      2.51       5
     N     765      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 4632
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4632
          Classifications: {'peptide': 597}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 32, 'TRANS': 564}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 221
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 15, 'ASN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 118
  Time building chain proxies: 3.31, per 1000 atoms: 0.71
  Number of scatterers: 4632
  At special positions: 0
  Unit cell: (69.39, 74.9412, 103.622, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     864      8.00
     N     765      7.00
     C    2979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 507 " - pdb=" SG  CYS A 538 " distance=2.67

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 615.5 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 9 sheets defined
      22.9% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 491 through 501
    Processing helix  chain 'A' and resid 516 through 522
      removed outlier: 3.816A  pdb=" N   HIS A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 546
      removed outlier: 4.175A  pdb=" N   GLY A 531 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 561 through 572
    Processing helix  chain 'A' and resid 573 through 576
    Processing helix  chain 'A' and resid 587 through 593
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 613 through 624
    Processing helix  chain 'A' and resid 649 through 672
      removed outlier: 3.593A  pdb=" N   ILE A 653 " --> pdb=" O   PRO A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 711
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117
      removed outlier: 6.584A  pdb=" N   LEU A 129 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163
      removed outlier: 6.515A  pdb=" N   LYS A 173 " --> pdb=" O   ASP A 159 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA A 171 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 163 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   TYR A 169 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   MET A 195 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 209
      removed outlier: 7.554A  pdb=" N   VAL A 202 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLN A 222 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 204 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   CYS A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   HIS A 228 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   THR A 246 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 230 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258
      removed outlier: 7.476A  pdb=" N   VAL A 277 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305
      removed outlier: 5.882A  pdb=" N   ARG A 326 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU A 339 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 354
      removed outlier: 6.958A  pdb=" N   PHE A 362 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 352 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   MET A 354 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   HIS A 358 " --> pdb=" O   MET A 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395
      removed outlier: 3.524A  pdb=" N   CYS A 409 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   SER A 410 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 445
      removed outlier: 6.257A  pdb=" N   LEU A 475 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   CYS A 507 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   HIS A 477 " --> pdb=" O   CYS A 507 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU A 474 " --> pdb=" O   THR A 554 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   THR A 556 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 476 " --> pdb=" O   THR A 556 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   PHE A 558 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   THR A 553 " --> pdb=" O   ALA A 578 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   THR A 580 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A 555 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   GLU A 582 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ALA A 557 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 449

    193 hydrogen bonds defined for protein.
    528 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: 1.50

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 881
        1.32 -     1.45: 1301
        1.45 -     1.57: 2530
        1.57 -     1.70: 3
        1.70 -     1.83: 34
  Bond restraints: 4749
  Sorted by residual:
  bond pdb=" CA  GLY A 513 "
       pdb=" C   GLY A 513 "
    ideal  model  delta    sigma   weight residual
    1.511  1.553 -0.042 1.03e-02 9.43e+03 1.67e+01
  bond pdb=" CA  ALA A 583 "
       pdb=" C   ALA A 583 "
    ideal  model  delta    sigma   weight residual
    1.534  1.496  0.038 9.50e-03 1.11e+04 1.58e+01
  bond pdb=" N   PRO A 584 "
       pdb=" CA  PRO A 584 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.047 1.19e-02 7.06e+03 1.58e+01
  bond pdb=" CB  HIS A 638 "
       pdb=" CG  HIS A 638 "
    ideal  model  delta    sigma   weight residual
    1.497  1.446  0.051 1.40e-02 5.10e+03 1.34e+01
  bond pdb=" C   ASN A 271 "
       pdb=" N   LYS A 272 "
    ideal  model  delta    sigma   weight residual
    1.333  1.278  0.054 1.50e-02 4.44e+03 1.32e+01
  ... (remaining 4744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 5813
        2.65 -     5.29: 588
        5.29 -     7.94: 62
        7.94 -    10.59: 7
       10.59 -    13.24: 1
  Bond angle restraints: 6471
  Sorted by residual:
  angle pdb=" C   ASP A 249 "
        pdb=" N   PRO A 250 "
        pdb=" CA  PRO A 250 "
      ideal   model   delta    sigma   weight residual
     119.56  127.86   -8.30 1.02e+00 9.61e-01 6.62e+01
  angle pdb=" C   THR A 331 "
        pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
      ideal   model   delta    sigma   weight residual
     119.56  127.40   -7.84 1.01e+00 9.80e-01 6.02e+01
  angle pdb=" C   ARG A 413 "
        pdb=" N   PRO A 414 "
        pdb=" CA  PRO A 414 "
      ideal   model   delta    sigma   weight residual
     119.66  125.07   -5.41 7.30e-01 1.88e+00 5.50e+01
  angle pdb=" C   PRO A 387 "
        pdb=" N   PRO A 388 "
        pdb=" CA  PRO A 388 "
      ideal   model   delta    sigma   weight residual
     119.56  126.87   -7.31 1.02e+00 9.61e-01 5.14e+01
  angle pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
        pdb=" C   ASN A 241 "
      ideal   model   delta    sigma   weight residual
     107.98  121.22  -13.24 1.88e+00 2.83e-01 4.96e+01
  ... (remaining 6466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2686
       17.98 -    35.96: 101
       35.96 -    53.95: 19
       53.95 -    71.93: 14
       71.93 -    89.91: 2
  Dihedral angle restraints: 2822
    sinusoidal: 1069
      harmonic: 1753
  Sorted by residual:
  dihedral pdb=" CA  ARG A 524 "
           pdb=" C   ARG A 524 "
           pdb=" N   LEU A 525 "
           pdb=" CA  LEU A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASP A 713 "
           pdb=" CB  ASP A 713 "
           pdb=" CG  ASP A 713 "
           pdb=" OD1 ASP A 713 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.32   57.32     1      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CB  GLU A 276 "
           pdb=" CG  GLU A 276 "
           pdb=" CD  GLU A 276 "
           pdb=" OE1 GLU A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.91  -89.91     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 2819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 324
       0.056 -    0.112: 222
       0.112 -    0.168: 126
       0.168 -    0.224: 44
       0.224 -    0.280: 16
  Chirality restraints: 732
  Sorted by residual:
  chirality pdb=" CG  LEU A 589 "
            pdb=" CB  LEU A 589 "
            pdb=" CD1 LEU A 589 "
            pdb=" CD2 LEU A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.87    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ILE A 269 "
            pdb=" N   ILE A 269 "
            pdb=" C   ILE A 269 "
            pdb=" CB  ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  LEU A 515 "
            pdb=" N   LEU A 515 "
            pdb=" C   LEU A 515 "
            pdb=" CB  LEU A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 729 not shown)

  Planarity restraints: 830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 519 "   -0.048 2.00e-02 2.50e+03   2.78e-02 1.93e+01
        pdb=" CG  TRP A 519 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 519 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 519 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 519 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 519 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 519 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 519 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 519 "    0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 519 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 257 "   -0.041 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR A 257 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 257 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 257 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 257 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 257 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 421 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LYS A 421 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS A 421 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A 422 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 827 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 240
        2.70 -     3.25: 4391
        3.25 -     3.80: 7328
        3.80 -     4.35: 9774
        4.35 -     4.90: 15427
  Nonbonded interactions: 37160
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 228 "
            pdb=" OD1 ASP A 229 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   GLU A 603 "
            pdb=" N   GLU A 606 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OD2 ASP A 396 "
            pdb=" ND2 ASN A 398 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" OD1 ASP A 210 "
            pdb=" OE1 GLU A 211 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" O   LYS A 168 "
            pdb=" N   LEU A 189 "
     model   vdw
     2.463 3.120
  ... (remaining 37155 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     15.270
  Find NCS groups from input model:        0.050
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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      :  0.015   0.076   4749  Z= 1.019
  Angle     :  1.676  13.235   6471  Z= 1.187
  Chirality :  0.096   0.280    732
  Planarity :  0.010   0.099    830
  Dihedral  : 11.236  89.908   1687
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  2.45 %
    Favored  : 95.50 %
  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:  0.42 (0.32), residues: 591
  helix:  0.82 (0.45), residues: 102
  sheet:  1.14 (0.36), residues: 181
  loop : -0.41 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.007   TRP A 519 
 HIS   0.008   0.002   HIS A 616 
 PHE   0.027   0.003   PHE A 218 
 TYR   0.042   0.006   TYR A 257 
 ARG   0.006   0.001   ARG A 510 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8855 (m100) cc_final: 0.8528 (m100)
REVERT: A  278 TRP cc_start: 0.8463 (m100) cc_final: 0.7825 (m100)
REVERT: A  291 LEU cc_start: 0.8252 (tp) cc_final: 0.8009 (tt)
REVERT: A  347 THR cc_start: 0.8325 (p) cc_final: 0.8070 (p)
REVERT: A  357 ASP cc_start: 0.7081 (m-30) cc_final: 0.6704 (m-30)
REVERT: A  427 LEU cc_start: 0.7624 (tp) cc_final: 0.7387 (pt)
REVERT: A  429 GLU cc_start: 0.7842 (mp0) cc_final: 0.7501 (mp0)
REVERT: A  462 HIS cc_start: 0.8286 (p90) cc_final: 0.7905 (p90)
REVERT: A  601 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8487 (tt)
REVERT: A  621 LYS cc_start: 0.8190 (tttt) cc_final: 0.7846 (tppt)
  outliers start: 10
  outliers final: 1
  residues processed: 217
  average time/residue: 0.1813
  time to fit residues: 49.1610
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 346 ASN
A 365 HIS
A 470 GLN
A 616 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.135938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109242 restraints weight = 8567.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113406 restraints weight = 4562.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116297 restraints weight = 2938.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4749  Z= 0.231
  Angle     :  0.678   6.857   6471  Z= 0.365
  Chirality :  0.047   0.169    732
  Planarity :  0.004   0.029    830
  Dihedral  :  5.149  20.692    639
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.09 %
    Favored  : 95.71 %
  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:  0.46 (0.33), residues: 591
  helix:  1.19 (0.46), residues: 113
  sheet:  0.76 (0.37), residues: 180
  loop : -0.27 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 502 
 HIS   0.004   0.001   HIS A 228 
 PHE   0.010   0.002   PHE A 705 
 TYR   0.029   0.002   TYR A 169 
 ARG   0.006   0.001   ARG A 223 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (t)
REVERT: A  187 ILE cc_start: 0.9148 (mm) cc_final: 0.8923 (mm)
REVERT: A  189 LEU cc_start: 0.8115 (mt) cc_final: 0.7705 (tp)
REVERT: A  207 TRP cc_start: 0.8658 (m100) cc_final: 0.8187 (m100)
REVERT: A  223 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7598 (ptp-170)
REVERT: A  230 VAL cc_start: 0.9239 (t) cc_final: 0.8942 (p)
REVERT: A  278 TRP cc_start: 0.8216 (m100) cc_final: 0.7854 (m100)
REVERT: A  346 ASN cc_start: 0.8579 (m-40) cc_final: 0.8215 (m-40)
REVERT: A  418 TYR cc_start: 0.6835 (m-80) cc_final: 0.6215 (m-80)
REVERT: A  427 LEU cc_start: 0.8414 (tp) cc_final: 0.7918 (pt)
REVERT: A  558 PHE cc_start: 0.8028 (t80) cc_final: 0.7707 (t80)
REVERT: A  601 LEU cc_start: 0.8980 (pp) cc_final: 0.8656 (tt)
REVERT: A  621 LYS cc_start: 0.8203 (tttt) cc_final: 0.7378 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1406
  time to fit residues: 29.6102
Evaluate side-chains
  106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0050
   chunk 30 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    2.9398

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
** A 477 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 = 0.3641 r_free = 0.3641 target = 0.127084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.099847 restraints weight = 8821.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.103571 restraints weight = 4916.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.106144 restraints weight = 3318.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   4749  Z= 0.380
  Angle     :  0.722   8.494   6471  Z= 0.384
  Chirality :  0.049   0.151    732
  Planarity :  0.004   0.035    830
  Dihedral  :  5.122  16.852    639
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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:  0.26 (0.33), residues: 591
  helix:  1.23 (0.47), residues: 113
  sheet:  0.77 (0.38), residues: 175
  loop : -0.57 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 502 
 HIS   0.009   0.002   HIS A 508 
 PHE   0.017   0.002   PHE A 362 
 TYR   0.012   0.002   TYR A 623 
 ARG   0.002   0.000   ARG A 510 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.8435 (pttm) cc_final: 0.8146 (ttpp)
REVERT: A  207 TRP cc_start: 0.8765 (m100) cc_final: 0.7813 (m100)
REVERT: A  217 LEU cc_start: 0.9247 (tp) cc_final: 0.8672 (tp)
REVERT: A  223 ARG cc_start: 0.7893 (ptp-110) cc_final: 0.7662 (ptp-110)
REVERT: A  245 TYR cc_start: 0.8313 (t80) cc_final: 0.8108 (t80)
REVERT: A  256 LEU cc_start: 0.9432 (mt) cc_final: 0.9134 (mt)
REVERT: A  278 TRP cc_start: 0.8326 (m100) cc_final: 0.7798 (m100)
REVERT: A  336 ASN cc_start: 0.8745 (m-40) cc_final: 0.8437 (t0)
REVERT: A  346 ASN cc_start: 0.8428 (m-40) cc_final: 0.8120 (m-40)
REVERT: A  354 MET cc_start: 0.8748 (tpp) cc_final: 0.8446 (tpt)
REVERT: A  389 TRP cc_start: 0.9295 (p-90) cc_final: 0.9047 (p-90)
REVERT: A  427 LEU cc_start: 0.8572 (tp) cc_final: 0.8128 (pt)
REVERT: A  462 HIS cc_start: 0.8534 (p90) cc_final: 0.8135 (p-80)
REVERT: A  500 ASP cc_start: 0.8504 (t70) cc_final: 0.8029 (t0)
REVERT: A  554 THR cc_start: 0.9370 (m) cc_final: 0.9067 (p)
REVERT: A  601 LEU cc_start: 0.9146 (pp) cc_final: 0.8748 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1655
  time to fit residues: 29.6937
Evaluate side-chains
  100 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 0 optimal weight:   40.0000
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.132382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.104462 restraints weight = 8765.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.108518 restraints weight = 4739.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111286 restraints weight = 3124.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4749  Z= 0.213
  Angle     :  0.586   7.419   6471  Z= 0.316
  Chirality :  0.045   0.161    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.864  17.493    639
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.34), residues: 591
  helix:  1.53 (0.48), residues: 113
  sheet:  0.83 (0.38), residues: 170
  loop : -0.46 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 607 
 HIS   0.002   0.001   HIS A 305 
 PHE   0.010   0.001   PHE A 362 
 TYR   0.032   0.002   TYR A 623 
 ARG   0.003   0.000   ARG A 382 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7364 (t) cc_final: 0.7098 (p)
REVERT: A  195 MET cc_start: 0.8466 (tmm) cc_final: 0.8150 (tmm)
REVERT: A  207 TRP cc_start: 0.8712 (m100) cc_final: 0.8419 (m100)
REVERT: A  223 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7584 (ptp-110)
REVERT: A  231 TYR cc_start: 0.7660 (m-80) cc_final: 0.7214 (m-10)
REVERT: A  238 ASN cc_start: 0.7642 (m-40) cc_final: 0.7423 (m-40)
REVERT: A  245 TYR cc_start: 0.8324 (t80) cc_final: 0.8065 (t80)
REVERT: A  336 ASN cc_start: 0.8715 (m-40) cc_final: 0.8406 (t0)
REVERT: A  346 ASN cc_start: 0.8205 (m-40) cc_final: 0.7763 (m-40)
REVERT: A  427 LEU cc_start: 0.8571 (tp) cc_final: 0.8129 (pt)
REVERT: A  462 HIS cc_start: 0.8542 (p90) cc_final: 0.8174 (p-80)
REVERT: A  477 HIS cc_start: 0.8225 (m170) cc_final: 0.8019 (m170)
REVERT: A  500 ASP cc_start: 0.8614 (t70) cc_final: 0.8076 (t0)
REVERT: A  519 TRP cc_start: 0.8589 (m100) cc_final: 0.8375 (m100)
REVERT: A  554 THR cc_start: 0.9369 (m) cc_final: 0.9159 (t)
REVERT: A  601 LEU cc_start: 0.9098 (pp) cc_final: 0.8748 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1356
  time to fit residues: 24.8975
Evaluate side-chains
  101 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 HIS
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.129136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.101895 restraints weight = 8950.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.105763 restraints weight = 4881.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108450 restraints weight = 3230.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4749  Z= 0.285
  Angle     :  0.632   7.433   6471  Z= 0.337
  Chirality :  0.046   0.152    732
  Planarity :  0.004   0.040    830
  Dihedral  :  4.966  16.501    639
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  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:  0.28 (0.34), residues: 591
  helix:  1.34 (0.49), residues: 113
  sheet:  0.78 (0.39), residues: 173
  loop : -0.59 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 389 
 HIS   0.005   0.002   HIS A 228 
 PHE   0.019   0.002   PHE A 705 
 TYR   0.015   0.002   TYR A 301 
 ARG   0.006   0.001   ARG A 442 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9364 (mt) cc_final: 0.9112 (mp)
REVERT: A  207 TRP cc_start: 0.8794 (m100) cc_final: 0.7857 (m100)
REVERT: A  217 LEU cc_start: 0.9270 (tp) cc_final: 0.8757 (tp)
REVERT: A  223 ARG cc_start: 0.7842 (ptp-110) cc_final: 0.7603 (ptp-110)
REVERT: A  231 TYR cc_start: 0.7659 (m-80) cc_final: 0.7179 (m-10)
REVERT: A  238 ASN cc_start: 0.7861 (m-40) cc_final: 0.7608 (m-40)
REVERT: A  245 TYR cc_start: 0.8256 (t80) cc_final: 0.7883 (t80)
REVERT: A  346 ASN cc_start: 0.8125 (m-40) cc_final: 0.7651 (m-40)
REVERT: A  370 TYR cc_start: 0.8171 (m-80) cc_final: 0.7892 (m-10)
REVERT: A  427 LEU cc_start: 0.8608 (tp) cc_final: 0.8158 (pt)
REVERT: A  462 HIS cc_start: 0.8865 (p90) cc_final: 0.8653 (p90)
REVERT: A  500 ASP cc_start: 0.8638 (t70) cc_final: 0.8163 (t0)
REVERT: A  519 TRP cc_start: 0.8686 (m100) cc_final: 0.8482 (m100)
REVERT: A  601 LEU cc_start: 0.9140 (pp) cc_final: 0.8813 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1263
  time to fit residues: 20.2994
Evaluate side-chains
  92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.100508 restraints weight = 8992.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.104354 restraints weight = 5075.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.106959 restraints weight = 3467.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4749  Z= 0.269
  Angle     :  0.600   6.852   6471  Z= 0.324
  Chirality :  0.046   0.173    732
  Planarity :  0.004   0.038    830
  Dihedral  :  4.846  16.376    639
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  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:  0.15 (0.34), residues: 591
  helix:  1.47 (0.49), residues: 114
  sheet:  0.67 (0.40), residues: 170
  loop : -0.76 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 389 
 HIS   0.003   0.001   HIS A 633 
 PHE   0.010   0.002   PHE A 362 
 TYR   0.015   0.001   TYR A 301 
 ARG   0.004   0.000   ARG A 577 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9354 (mt) cc_final: 0.9095 (mp)
REVERT: A  167 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8318 (mt-10)
REVERT: A  207 TRP cc_start: 0.8804 (m100) cc_final: 0.7894 (m100)
REVERT: A  217 LEU cc_start: 0.9262 (tp) cc_final: 0.8737 (tp)
REVERT: A  223 ARG cc_start: 0.7753 (ptp-110) cc_final: 0.7515 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7690 (m-80) cc_final: 0.7249 (m-10)
REVERT: A  245 TYR cc_start: 0.8199 (t80) cc_final: 0.7726 (t80)
REVERT: A  346 ASN cc_start: 0.8052 (m-40) cc_final: 0.7593 (m-40)
REVERT: A  427 LEU cc_start: 0.8673 (tp) cc_final: 0.8207 (pt)
REVERT: A  462 HIS cc_start: 0.8929 (p90) cc_final: 0.8707 (p90)
REVERT: A  490 PHE cc_start: 0.9213 (t80) cc_final: 0.8939 (t80)
REVERT: A  500 ASP cc_start: 0.8704 (t70) cc_final: 0.8280 (t0)
REVERT: A  601 LEU cc_start: 0.9177 (pp) cc_final: 0.8864 (tt)
REVERT: A  624 CYS cc_start: 0.8943 (t) cc_final: 0.8668 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1517
  time to fit residues: 23.3364
Evaluate side-chains
  95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.123467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.094954 restraints weight = 9156.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.098383 restraints weight = 5391.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.100739 restraints weight = 3789.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   4749  Z= 0.454
  Angle     :  0.742   8.719   6471  Z= 0.391
  Chirality :  0.049   0.138    732
  Planarity :  0.005   0.036    830
  Dihedral  :  5.325  19.082    639
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.34 (0.33), residues: 591
  helix:  1.24 (0.48), residues: 111
  sheet:  0.36 (0.40), residues: 169
  loop : -1.12 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 519 
 HIS   0.019   0.003   HIS A 228 
 PHE   0.019   0.002   PHE A 490 
 TYR   0.018   0.002   TYR A 506 
 ARG   0.008   0.001   ARG A 510 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7773 (t) cc_final: 0.7436 (p)
REVERT: A  145 LEU cc_start: 0.9354 (mt) cc_final: 0.9129 (mp)
REVERT: A  189 LEU cc_start: 0.8169 (mt) cc_final: 0.7922 (mt)
REVERT: A  195 MET cc_start: 0.8615 (tmm) cc_final: 0.8370 (tmm)
REVERT: A  207 TRP cc_start: 0.8854 (m100) cc_final: 0.8214 (m100)
REVERT: A  217 LEU cc_start: 0.9308 (tp) cc_final: 0.9011 (tp)
REVERT: A  223 ARG cc_start: 0.7696 (ptp-110) cc_final: 0.7440 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7819 (m-80) cc_final: 0.7393 (m-10)
REVERT: A  245 TYR cc_start: 0.8151 (t80) cc_final: 0.7651 (t80)
REVERT: A  346 ASN cc_start: 0.8154 (m-40) cc_final: 0.7775 (m-40)
REVERT: A  462 HIS cc_start: 0.9002 (p90) cc_final: 0.8691 (p90)
REVERT: A  601 LEU cc_start: 0.9236 (pp) cc_final: 0.8917 (tt)
REVERT: A  624 CYS cc_start: 0.8892 (t) cc_final: 0.8650 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1414
  time to fit residues: 18.4849
Evaluate side-chains
  78 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.098250 restraints weight = 9071.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.101939 restraints weight = 5167.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.104435 restraints weight = 3563.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4749  Z= 0.261
  Angle     :  0.614   5.799   6471  Z= 0.329
  Chirality :  0.045   0.147    732
  Planarity :  0.004   0.037    830
  Dihedral  :  5.000  16.568    639
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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: -0.10 (0.34), residues: 591
  helix:  1.69 (0.49), residues: 113
  sheet:  0.36 (0.40), residues: 167
  loop : -0.98 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 389 
 HIS   0.011   0.002   HIS A 228 
 PHE   0.011   0.001   PHE A 120 
 TYR   0.013   0.001   TYR A 169 
 ARG   0.003   0.000   ARG A 494 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7805 (t) cc_final: 0.7461 (p)
REVERT: A  145 LEU cc_start: 0.9333 (mt) cc_final: 0.9122 (mp)
REVERT: A  189 LEU cc_start: 0.8144 (mt) cc_final: 0.7903 (mt)
REVERT: A  195 MET cc_start: 0.8548 (tmm) cc_final: 0.8278 (tmm)
REVERT: A  207 TRP cc_start: 0.8826 (m100) cc_final: 0.8006 (m100)
REVERT: A  217 LEU cc_start: 0.9243 (tp) cc_final: 0.8971 (tp)
REVERT: A  223 ARG cc_start: 0.7707 (ptp-110) cc_final: 0.7486 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7832 (m-80) cc_final: 0.7471 (m-10)
REVERT: A  245 TYR cc_start: 0.8254 (t80) cc_final: 0.7742 (t80)
REVERT: A  256 LEU cc_start: 0.9318 (mt) cc_final: 0.9035 (mt)
REVERT: A  346 ASN cc_start: 0.7993 (m-40) cc_final: 0.7588 (m-40)
REVERT: A  427 LEU cc_start: 0.8442 (tp) cc_final: 0.7880 (pt)
REVERT: A  462 HIS cc_start: 0.8988 (p90) cc_final: 0.8768 (p90)
REVERT: A  488 MET cc_start: 0.8859 (mmm) cc_final: 0.8055 (mmm)
REVERT: A  500 ASP cc_start: 0.8815 (t0) cc_final: 0.8546 (t0)
REVERT: A  601 LEU cc_start: 0.9184 (pp) cc_final: 0.8869 (tt)
REVERT: A  624 CYS cc_start: 0.8900 (t) cc_final: 0.8631 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1525
  time to fit residues: 20.0963
Evaluate side-chains
  85 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.101310 restraints weight = 8921.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.105114 restraints weight = 4981.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.107687 restraints weight = 3383.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.6085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4749  Z= 0.176
  Angle     :  0.582   5.957   6471  Z= 0.308
  Chirality :  0.045   0.150    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.676  16.633    639
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  0.11 (0.34), residues: 591
  helix:  1.93 (0.50), residues: 113
  sheet:  0.44 (0.40), residues: 169
  loop : -0.85 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 389 
 HIS   0.014   0.001   HIS A 228 
 PHE   0.011   0.001   PHE A 120 
 TYR   0.015   0.001   TYR A 169 
 ARG   0.004   0.000   ARG A 223 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7746 (t) cc_final: 0.7413 (p)
REVERT: A  145 LEU cc_start: 0.9342 (mt) cc_final: 0.9107 (mp)
REVERT: A  173 LYS cc_start: 0.7825 (pttm) cc_final: 0.7529 (ptpp)
REVERT: A  189 LEU cc_start: 0.8147 (mt) cc_final: 0.7938 (mt)
REVERT: A  207 TRP cc_start: 0.8780 (m100) cc_final: 0.7852 (m100)
REVERT: A  217 LEU cc_start: 0.9157 (tp) cc_final: 0.8926 (tp)
REVERT: A  231 TYR cc_start: 0.7712 (m-80) cc_final: 0.7302 (m-10)
REVERT: A  245 TYR cc_start: 0.8277 (t80) cc_final: 0.7724 (t80)
REVERT: A  346 ASN cc_start: 0.7825 (m-40) cc_final: 0.7435 (m-40)
REVERT: A  347 THR cc_start: 0.9108 (m) cc_final: 0.8699 (p)
REVERT: A  427 LEU cc_start: 0.8526 (tp) cc_final: 0.7939 (pt)
REVERT: A  462 HIS cc_start: 0.8967 (p90) cc_final: 0.8710 (p90)
REVERT: A  488 MET cc_start: 0.8737 (mmm) cc_final: 0.7843 (mmm)
REVERT: A  500 ASP cc_start: 0.8929 (t0) cc_final: 0.8528 (t0)
REVERT: A  601 LEU cc_start: 0.9203 (pp) cc_final: 0.8893 (tt)
REVERT: A  621 LYS cc_start: 0.8559 (tttt) cc_final: 0.7915 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1473
  time to fit residues: 20.8314
Evaluate side-chains
  83 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0670
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0920

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.130343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.101348 restraints weight = 8986.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.105161 restraints weight = 5098.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.107725 restraints weight = 3470.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.6198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4749  Z= 0.195
  Angle     :  0.581   5.788   6471  Z= 0.308
  Chirality :  0.045   0.149    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.610  15.952    639
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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:  0.14 (0.34), residues: 591
  helix:  1.91 (0.51), residues: 112
  sheet:  0.50 (0.40), residues: 168
  loop : -0.83 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 389 
 HIS   0.013   0.001   HIS A 228 
 PHE   0.011   0.001   PHE A 120 
 TYR   0.011   0.001   TYR A 301 
 ARG   0.007   0.001   ARG A 223 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7794 (t) cc_final: 0.7455 (p)
REVERT: A  145 LEU cc_start: 0.9355 (mt) cc_final: 0.9130 (mp)
REVERT: A  173 LYS cc_start: 0.7862 (pttm) cc_final: 0.7558 (ptpp)
REVERT: A  207 TRP cc_start: 0.8809 (m100) cc_final: 0.7954 (m100)
REVERT: A  217 LEU cc_start: 0.9193 (tp) cc_final: 0.8952 (tp)
REVERT: A  231 TYR cc_start: 0.7744 (m-80) cc_final: 0.7457 (m-10)
REVERT: A  245 TYR cc_start: 0.8287 (t80) cc_final: 0.7727 (t80)
REVERT: A  346 ASN cc_start: 0.7829 (m-40) cc_final: 0.7578 (m-40)
REVERT: A  347 THR cc_start: 0.9137 (m) cc_final: 0.8640 (p)
REVERT: A  365 HIS cc_start: 0.7290 (t70) cc_final: 0.6747 (t70)
REVERT: A  427 LEU cc_start: 0.8486 (tp) cc_final: 0.7909 (pt)
REVERT: A  462 HIS cc_start: 0.8928 (p90) cc_final: 0.8670 (p90)
REVERT: A  488 MET cc_start: 0.8782 (mmm) cc_final: 0.8018 (mmm)
REVERT: A  500 ASP cc_start: 0.8915 (t0) cc_final: 0.8564 (t0)
REVERT: A  601 LEU cc_start: 0.9199 (pp) cc_final: 0.8896 (tt)
REVERT: A  621 LYS cc_start: 0.8686 (tttt) cc_final: 0.7935 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1480
  time to fit residues: 20.1184
Evaluate side-chains
  85 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.102835 restraints weight = 8946.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.106673 restraints weight = 5020.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.109257 restraints weight = 3410.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4749  Z= 0.165
  Angle     :  0.559   5.745   6471  Z= 0.296
  Chirality :  0.044   0.154    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.460  15.629    639
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  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 (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:  0.23 (0.34), residues: 591
  helix:  1.91 (0.51), residues: 113
  sheet:  0.47 (0.40), residues: 170
  loop : -0.69 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 389 
 HIS   0.009   0.001   HIS A 228 
 PHE   0.011   0.001   PHE A 120 
 TYR   0.010   0.001   TYR A 301 
 ARG   0.001   0.000   ARG A 495 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1705.45 seconds
wall clock time: 31 minutes 32.86 seconds (1892.86 seconds total)