Starting phenix.real_space_refine
on Thu Mar  6 02:54:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rfb_19117/03_2025/8rfb_19117_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rfb_19117/03_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_19117/03_2025/8rfb_19117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rfb_19117/03_2025/8rfb_19117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rfb_19117/03_2025/8rfb_19117_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rfb_19117/03_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-5624/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: 3.38, per 1000 atoms: 0.73
  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: 1.32
  Conformation dependent library (CDL) restraints added in 588.6 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: 0.70
  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: 1.48 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:             0.470
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.600
-------------------------------------------------------------------------------
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  : 0.484 
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: 0.1666
  time to fit residues: 45.0024
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  : 0.496 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   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 = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113407 restraints weight = 4562.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.116290 restraints weight = 2938.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
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  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8277 (t)
REVERT: A  187 ILE cc_start: 0.9149 (mm) cc_final: 0.8923 (mm)
REVERT: A  189 LEU cc_start: 0.8116 (mt) cc_final: 0.7705 (tp)
REVERT: A  207 TRP cc_start: 0.8658 (m100) cc_final: 0.8188 (m100)
REVERT: A  223 ARG cc_start: 0.7961 (ptp-110) cc_final: 0.7598 (ptp-170)
REVERT: A  230 VAL cc_start: 0.9240 (t) cc_final: 0.8944 (p)
REVERT: A  278 TRP cc_start: 0.8217 (m100) cc_final: 0.7854 (m100)
REVERT: A  346 ASN cc_start: 0.8575 (m-40) cc_final: 0.8215 (m-40)
REVERT: A  418 TYR cc_start: 0.6834 (m-80) cc_final: 0.6215 (m-80)
REVERT: A  427 LEU cc_start: 0.8411 (tp) cc_final: 0.7916 (pt)
REVERT: A  558 PHE cc_start: 0.8028 (t80) cc_final: 0.7706 (t80)
REVERT: A  601 LEU cc_start: 0.8979 (pp) cc_final: 0.8655 (tt)
REVERT: A  621 LYS cc_start: 0.8204 (tttt) cc_final: 0.7381 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1335
  time to fit residues: 28.0107
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  : 0.504 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   overall best weight:    3.1798

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.126469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.099148 restraints weight = 8859.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.102936 restraints weight = 4910.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.105521 restraints weight = 3286.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4749  Z= 0.400
  Angle     :  0.738   8.341   6471  Z= 0.391
  Chirality :  0.049   0.153    732
  Planarity :  0.004   0.034    830
  Dihedral  :  5.183  17.522    639
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  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:  0.21 (0.33), residues: 591
  helix:  1.20 (0.47), residues: 113
  sheet:  0.74 (0.38), residues: 175
  loop : -0.61 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 519 
 HIS   0.023   0.003   HIS A 228 
 PHE   0.018   0.002   PHE A 362 
 TYR   0.023   0.002   TYR A 219 
 ARG   0.003   0.001   ARG A 226 

*********************** 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
  134 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.8452 (pttm) cc_final: 0.8186 (ttpp)
REVERT: A  207 TRP cc_start: 0.8773 (m100) cc_final: 0.7824 (m100)
REVERT: A  217 LEU cc_start: 0.9238 (tp) cc_final: 0.8651 (tp)
REVERT: A  223 ARG cc_start: 0.7901 (ptp-110) cc_final: 0.7664 (ptp-110)
REVERT: A  245 TYR cc_start: 0.8326 (t80) cc_final: 0.8074 (t80)
REVERT: A  256 LEU cc_start: 0.9442 (mt) cc_final: 0.9135 (mt)
REVERT: A  278 TRP cc_start: 0.8318 (m100) cc_final: 0.7797 (m100)
REVERT: A  346 ASN cc_start: 0.8447 (m-40) cc_final: 0.8154 (m-40)
REVERT: A  389 TRP cc_start: 0.9306 (p-90) cc_final: 0.9040 (p-90)
REVERT: A  427 LEU cc_start: 0.8562 (tp) cc_final: 0.8109 (pt)
REVERT: A  462 HIS cc_start: 0.8560 (p90) cc_final: 0.8165 (p-80)
REVERT: A  500 ASP cc_start: 0.8495 (t70) cc_final: 0.8027 (t0)
REVERT: A  519 TRP cc_start: 0.8706 (m100) cc_final: 0.8392 (m100)
REVERT: A  554 THR cc_start: 0.9377 (m) cc_final: 0.9074 (p)
REVERT: A  601 LEU cc_start: 0.9150 (pp) cc_final: 0.8757 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1516
  time to fit residues: 26.3379
Evaluate side-chains
  99 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:   40.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 628 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.131777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103691 restraints weight = 8884.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107701 restraints weight = 4870.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.110469 restraints weight = 3236.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4749  Z= 0.222
  Angle     :  0.597   7.477   6471  Z= 0.319
  Chirality :  0.045   0.159    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.886  17.427    639
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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:  0.40 (0.34), residues: 591
  helix:  1.59 (0.48), residues: 113
  sheet:  0.78 (0.39), residues: 170
  loop : -0.51 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 607 
 HIS   0.003   0.001   HIS A 305 
 PHE   0.014   0.001   PHE A 705 
 TYR   0.033   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
  129 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7395 (t) cc_final: 0.7122 (p)
REVERT: A  187 ILE cc_start: 0.9165 (mm) cc_final: 0.8936 (mm)
REVERT: A  195 MET cc_start: 0.8533 (tmm) cc_final: 0.8276 (tmm)
REVERT: A  207 TRP cc_start: 0.8745 (m100) cc_final: 0.7795 (m100)
REVERT: A  217 LEU cc_start: 0.9204 (tp) cc_final: 0.8787 (tp)
REVERT: A  223 ARG cc_start: 0.7876 (ptp-110) cc_final: 0.7622 (ptp-110)
REVERT: A  231 TYR cc_start: 0.7621 (m-80) cc_final: 0.7206 (m-10)
REVERT: A  238 ASN cc_start: 0.7708 (m-40) cc_final: 0.7485 (m-40)
REVERT: A  245 TYR cc_start: 0.8279 (t80) cc_final: 0.8043 (t80)
REVERT: A  336 ASN cc_start: 0.8711 (m-40) cc_final: 0.8494 (t0)
REVERT: A  346 ASN cc_start: 0.8147 (m-40) cc_final: 0.7663 (m-40)
REVERT: A  427 LEU cc_start: 0.8564 (tp) cc_final: 0.8128 (pt)
REVERT: A  500 ASP cc_start: 0.8629 (t70) cc_final: 0.8097 (t0)
REVERT: A  519 TRP cc_start: 0.8586 (m100) cc_final: 0.8377 (m100)
REVERT: A  554 THR cc_start: 0.9361 (m) cc_final: 0.9149 (t)
REVERT: A  601 LEU cc_start: 0.9107 (pp) cc_final: 0.8757 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1307
  time to fit residues: 22.9071
Evaluate side-chains
  102 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   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 365 HIS
A 628 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.105916 restraints weight = 8907.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109980 restraints weight = 4800.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112779 restraints weight = 3167.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4749  Z= 0.175
  Angle     :  0.577   7.312   6471  Z= 0.307
  Chirality :  0.045   0.155    732
  Planarity :  0.004   0.038    830
  Dihedral  :  4.715  16.876    639
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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:  0.39 (0.34), residues: 591
  helix:  1.51 (0.49), residues: 114
  sheet:  0.72 (0.41), residues: 167
  loop : -0.45 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 389 
 HIS   0.002   0.001   HIS A 477 
 PHE   0.011   0.001   PHE A 340 
 TYR   0.018   0.001   TYR A 623 
 ARG   0.004   0.000   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
  129 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9340 (mt) cc_final: 0.9073 (mp)
REVERT: A  189 LEU cc_start: 0.8156 (mt) cc_final: 0.7802 (tp)
REVERT: A  207 TRP cc_start: 0.8693 (m100) cc_final: 0.8388 (m100)
REVERT: A  223 ARG cc_start: 0.7873 (ptp-110) cc_final: 0.7605 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7515 (m-80) cc_final: 0.6980 (m-10)
REVERT: A  238 ASN cc_start: 0.7708 (m-40) cc_final: 0.7492 (m-40)
REVERT: A  245 TYR cc_start: 0.8342 (t80) cc_final: 0.7935 (t80)
REVERT: A  327 THR cc_start: 0.7360 (m) cc_final: 0.6543 (m)
REVERT: A  346 ASN cc_start: 0.7914 (m-40) cc_final: 0.7428 (m-40)
REVERT: A  370 TYR cc_start: 0.8066 (m-80) cc_final: 0.7788 (m-10)
REVERT: A  427 LEU cc_start: 0.8562 (tp) cc_final: 0.8114 (pt)
REVERT: A  500 ASP cc_start: 0.8657 (t70) cc_final: 0.8121 (t0)
REVERT: A  554 THR cc_start: 0.9320 (m) cc_final: 0.9113 (t)
REVERT: A  601 LEU cc_start: 0.9108 (pp) cc_final: 0.8779 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1326
  time to fit residues: 23.1835
Evaluate side-chains
  99 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 41 optimal weight:    0.2980
   chunk 1 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
A 365 HIS
A 628 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.134491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.106187 restraints weight = 8751.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.110210 restraints weight = 4797.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112925 restraints weight = 3201.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4749  Z= 0.165
  Angle     :  0.575   6.811   6471  Z= 0.310
  Chirality :  0.045   0.154    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.564  16.759    639
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.39 (0.34), residues: 591
  helix:  1.67 (0.50), residues: 114
  sheet:  0.80 (0.39), residues: 176
  loop : -0.62 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 519 
 HIS   0.007   0.001   HIS A 462 
 PHE   0.014   0.001   PHE A 705 
 TYR   0.023   0.001   TYR A 623 
 ARG   0.005   0.001   ARG A 622 

*********************** 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
  125 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.9328 (mt) cc_final: 0.9034 (mp)
REVERT: A  167 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: A  207 TRP cc_start: 0.8675 (m100) cc_final: 0.7666 (m100)
REVERT: A  217 LEU cc_start: 0.9189 (tp) cc_final: 0.8845 (tp)
REVERT: A  223 ARG cc_start: 0.7880 (ptp-110) cc_final: 0.7562 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7496 (m-80) cc_final: 0.7054 (m-10)
REVERT: A  238 ASN cc_start: 0.7738 (m-40) cc_final: 0.7503 (m-40)
REVERT: A  245 TYR cc_start: 0.8188 (t80) cc_final: 0.7768 (t80)
REVERT: A  346 ASN cc_start: 0.7894 (m-40) cc_final: 0.7447 (m-40)
REVERT: A  347 THR cc_start: 0.8973 (m) cc_final: 0.8478 (p)
REVERT: A  367 ASN cc_start: 0.8846 (t0) cc_final: 0.8434 (t0)
REVERT: A  370 TYR cc_start: 0.7976 (m-80) cc_final: 0.7735 (m-10)
REVERT: A  427 LEU cc_start: 0.8620 (tp) cc_final: 0.8155 (pt)
REVERT: A  500 ASP cc_start: 0.8704 (t70) cc_final: 0.8184 (t0)
REVERT: A  554 THR cc_start: 0.9335 (m) cc_final: 0.9119 (t)
REVERT: A  601 LEU cc_start: 0.9127 (pp) cc_final: 0.8839 (tt)
REVERT: A  621 LYS cc_start: 0.8258 (tttt) cc_final: 0.7908 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1320
  time to fit residues: 22.3508
Evaluate side-chains
  102 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
A 365 HIS
A 508 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.101970 restraints weight = 8881.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.105849 restraints weight = 4917.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108481 restraints weight = 3312.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5458

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= 0.235
  Angle     :  0.583   6.386   6471  Z= 0.315
  Chirality :  0.045   0.146    732
  Planarity :  0.004   0.035    830
  Dihedral  :  4.599  15.418    639
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.39 (0.34), residues: 591
  helix:  1.73 (0.50), residues: 114
  sheet:  0.77 (0.39), residues: 175
  loop : -0.62 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 519 
 HIS   0.004   0.001   HIS A 228 
 PHE   0.009   0.001   PHE A 120 
 TYR   0.017   0.001   TYR A 623 
 ARG   0.002   0.000   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
  125 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7591 (t) cc_final: 0.7364 (p)
REVERT: A  145 LEU cc_start: 0.9331 (mt) cc_final: 0.9084 (mp)
REVERT: A  207 TRP cc_start: 0.8742 (m100) cc_final: 0.7784 (m100)
REVERT: A  217 LEU cc_start: 0.9231 (tp) cc_final: 0.8732 (tp)
REVERT: A  223 ARG cc_start: 0.7785 (ptp-110) cc_final: 0.7499 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7620 (m-80) cc_final: 0.7204 (m-10)
REVERT: A  238 ASN cc_start: 0.8019 (m-40) cc_final: 0.7779 (m-40)
REVERT: A  245 TYR cc_start: 0.8151 (t80) cc_final: 0.7616 (t80)
REVERT: A  346 ASN cc_start: 0.7966 (m-40) cc_final: 0.7527 (m-40)
REVERT: A  365 HIS cc_start: 0.7329 (t70) cc_final: 0.6395 (t70)
REVERT: A  370 TYR cc_start: 0.8097 (m-80) cc_final: 0.7849 (m-10)
REVERT: A  427 LEU cc_start: 0.8740 (tp) cc_final: 0.8270 (pt)
REVERT: A  488 MET cc_start: 0.8800 (mmm) cc_final: 0.7817 (mmm)
REVERT: A  500 ASP cc_start: 0.8753 (t70) cc_final: 0.8346 (t0)
REVERT: A  554 THR cc_start: 0.9331 (m) cc_final: 0.9100 (t)
REVERT: A  558 PHE cc_start: 0.8263 (t80) cc_final: 0.7830 (t80)
REVERT: A  559 SER cc_start: 0.9511 (p) cc_final: 0.9258 (p)
REVERT: A  601 LEU cc_start: 0.9165 (pp) cc_final: 0.8868 (tt)
REVERT: A  621 LYS cc_start: 0.8674 (tttt) cc_final: 0.7984 (tppt)
REVERT: A  624 CYS cc_start: 0.8940 (t) cc_final: 0.8583 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1213
  time to fit residues: 20.4715
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  : 0.485 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0070
   chunk 53 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8004

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.132556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.103758 restraints weight = 8961.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107706 restraints weight = 4931.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110437 restraints weight = 3317.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4749  Z= 0.162
  Angle     :  0.564   6.281   6471  Z= 0.301
  Chirality :  0.045   0.154    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.452  17.018    639
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  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:  0.43 (0.34), residues: 591
  helix:  1.79 (0.50), residues: 114
  sheet:  0.81 (0.39), residues: 175
  loop : -0.62 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 389 
 HIS   0.005   0.001   HIS A 477 
 PHE   0.013   0.001   PHE A 705 
 TYR   0.023   0.001   TYR A 623 
 ARG   0.002   0.000   ARG A 622 

*********************** 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
  115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7708 (t) cc_final: 0.7483 (p)
REVERT: A  145 LEU cc_start: 0.9322 (mt) cc_final: 0.9077 (mp)
REVERT: A  207 TRP cc_start: 0.8659 (m100) cc_final: 0.7702 (m100)
REVERT: A  217 LEU cc_start: 0.9201 (tp) cc_final: 0.8725 (tp)
REVERT: A  231 TYR cc_start: 0.7615 (m-80) cc_final: 0.7324 (m-10)
REVERT: A  238 ASN cc_start: 0.7986 (m-40) cc_final: 0.7745 (m-40)
REVERT: A  245 TYR cc_start: 0.8133 (t80) cc_final: 0.7681 (t80)
REVERT: A  346 ASN cc_start: 0.7850 (m-40) cc_final: 0.7470 (m-40)
REVERT: A  347 THR cc_start: 0.8979 (m) cc_final: 0.8426 (p)
REVERT: A  365 HIS cc_start: 0.7303 (t70) cc_final: 0.6646 (t70)
REVERT: A  427 LEU cc_start: 0.8693 (tp) cc_final: 0.8229 (pt)
REVERT: A  488 MET cc_start: 0.8653 (mmm) cc_final: 0.7672 (mmm)
REVERT: A  500 ASP cc_start: 0.8781 (t70) cc_final: 0.8372 (t0)
REVERT: A  554 THR cc_start: 0.9350 (m) cc_final: 0.9119 (t)
REVERT: A  558 PHE cc_start: 0.8249 (t80) cc_final: 0.7926 (t80)
REVERT: A  601 LEU cc_start: 0.9136 (pp) cc_final: 0.8864 (tt)
REVERT: A  621 LYS cc_start: 0.8532 (tttt) cc_final: 0.7938 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1352
  time to fit residues: 20.9033
Evaluate side-chains
  99 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.130923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.102542 restraints weight = 8977.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.106388 restraints weight = 4907.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108977 restraints weight = 3280.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4749  Z= 0.169
  Angle     :  0.553   6.034   6471  Z= 0.294
  Chirality :  0.044   0.152    732
  Planarity :  0.003   0.036    830
  Dihedral  :  4.393  15.885    639
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  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:  0.52 (0.34), residues: 591
  helix:  1.99 (0.51), residues: 112
  sheet:  0.88 (0.39), residues: 178
  loop : -0.62 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 389 
 HIS   0.002   0.001   HIS A 477 
 PHE   0.010   0.001   PHE A 120 
 TYR   0.011   0.001   TYR A 301 
 ARG   0.003   0.000   ARG A 495 

*********************** 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
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7774 (t) cc_final: 0.7529 (p)
REVERT: A  145 LEU cc_start: 0.9364 (mt) cc_final: 0.9125 (mp)
REVERT: A  195 MET cc_start: 0.8250 (tmm) cc_final: 0.8012 (tmm)
REVERT: A  207 TRP cc_start: 0.8657 (m100) cc_final: 0.7734 (m100)
REVERT: A  217 LEU cc_start: 0.9210 (tp) cc_final: 0.8715 (tp)
REVERT: A  231 TYR cc_start: 0.7647 (m-80) cc_final: 0.7367 (m-10)
REVERT: A  238 ASN cc_start: 0.8004 (m-40) cc_final: 0.7763 (m-40)
REVERT: A  245 TYR cc_start: 0.8179 (t80) cc_final: 0.7652 (t80)
REVERT: A  346 ASN cc_start: 0.7847 (m-40) cc_final: 0.7445 (m-40)
REVERT: A  347 THR cc_start: 0.8965 (m) cc_final: 0.8419 (p)
REVERT: A  365 HIS cc_start: 0.7333 (t70) cc_final: 0.6716 (t70)
REVERT: A  427 LEU cc_start: 0.8709 (tp) cc_final: 0.8235 (pt)
REVERT: A  488 MET cc_start: 0.8621 (mmm) cc_final: 0.7751 (mmm)
REVERT: A  490 PHE cc_start: 0.9115 (t80) cc_final: 0.8800 (t80)
REVERT: A  495 ARG cc_start: 0.8713 (tpt-90) cc_final: 0.8389 (tpt-90)
REVERT: A  500 ASP cc_start: 0.8814 (t70) cc_final: 0.8501 (t0)
REVERT: A  504 LEU cc_start: 0.8544 (mp) cc_final: 0.8333 (mp)
REVERT: A  554 THR cc_start: 0.9340 (m) cc_final: 0.9056 (p)
REVERT: A  558 PHE cc_start: 0.8290 (t80) cc_final: 0.7924 (t80)
REVERT: A  601 LEU cc_start: 0.9135 (pp) cc_final: 0.8886 (tt)
REVERT: A  621 LYS cc_start: 0.8570 (tttt) cc_final: 0.7906 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1313
  time to fit residues: 20.2630
Evaluate side-chains
  97 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.127156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.098808 restraints weight = 9050.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.102483 restraints weight = 5065.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.104969 restraints weight = 3454.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4749  Z= 0.327
  Angle     :  0.657   6.975   6471  Z= 0.350
  Chirality :  0.046   0.153    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.838  16.723    639
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.33), residues: 591
  helix:  1.77 (0.50), residues: 113
  sheet:  0.63 (0.40), residues: 168
  loop : -0.84 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 389 
 HIS   0.007   0.002   HIS A 508 
 PHE   0.014   0.002   PHE A 490 
 TYR   0.017   0.002   TYR A 623 
 ARG   0.002   0.000   ARG A 345 

********************** 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
  105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7847 (t) cc_final: 0.7556 (p)
REVERT: A  207 TRP cc_start: 0.8802 (m100) cc_final: 0.8031 (m100)
REVERT: A  217 LEU cc_start: 0.9297 (tp) cc_final: 0.8915 (tp)
REVERT: A  231 TYR cc_start: 0.7770 (m-80) cc_final: 0.7524 (m-10)
REVERT: A  245 TYR cc_start: 0.8121 (t80) cc_final: 0.7667 (t80)
REVERT: A  346 ASN cc_start: 0.7929 (m-40) cc_final: 0.7579 (m-40)
REVERT: A  365 HIS cc_start: 0.7354 (t70) cc_final: 0.6662 (t70)
REVERT: A  427 LEU cc_start: 0.8666 (tp) cc_final: 0.8196 (pt)
REVERT: A  462 HIS cc_start: 0.8804 (p90) cc_final: 0.8572 (p90)
REVERT: A  495 ARG cc_start: 0.8879 (tpt-90) cc_final: 0.8570 (tpt-90)
REVERT: A  554 THR cc_start: 0.9398 (m) cc_final: 0.9163 (t)
REVERT: A  558 PHE cc_start: 0.8540 (t80) cc_final: 0.8304 (t80)
REVERT: A  601 LEU cc_start: 0.9193 (pp) cc_final: 0.8931 (tt)
REVERT: A  621 LYS cc_start: 0.8728 (tttt) cc_final: 0.8137 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1448
  time to fit residues: 20.1990
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  : 0.599 
-------------------------------------------------------------------------------
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:    0.0020
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0170
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5228

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.131644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.102597 restraints weight = 8911.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.106491 restraints weight = 4939.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109102 restraints weight = 3339.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.6044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4749  Z= 0.159
  Angle     :  0.577   5.690   6471  Z= 0.307
  Chirality :  0.044   0.155    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.538  16.120    639
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.85
  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:  0.40 (0.34), residues: 591
  helix:  2.07 (0.51), residues: 113
  sheet:  0.72 (0.39), residues: 176
  loop : -0.72 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 389 
 HIS   0.003   0.001   HIS A 633 
 PHE   0.009   0.001   PHE A 120 
 TYR   0.011   0.001   TYR A 301 
 ARG   0.006   0.001   ARG A 223 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1725.91 seconds
wall clock time: 30 minutes 52.41 seconds (1852.41 seconds total)