Starting phenix.real_space_refine
on Thu Mar  6 09:20:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yqm_34029/03_2025/7yqm_34029.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
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      29      5.16       5
     C    3543      2.51       5
     N    1015      2.21       5
     O    1069      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 5656
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 723, 5656
          Classifications: {'peptide': 723}
          Link IDs: {'PTRANS': 31, 'TRANS': 691}
  Time building chain proxies: 3.98, per 1000 atoms: 0.70
  Number of scatterers: 5656
  At special positions: 0
  Unit cell: (76.446, 81.378, 93.708, 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      29     16.00
     O    1069      8.00
     N    1015      7.00
     C    3543      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 866.5 milliseconds
  

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      53.0% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 24
    Processing helix  chain 'A' and resid 31 through 71
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 106 through 111
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 159 through 178
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 279 through 296
    Processing helix  chain 'A' and resid 359 through 378
      removed outlier: 4.224A  pdb=" N   TYR A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP A 374 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 414
      removed outlier: 4.033A  pdb=" N   GLU A 398 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 434 through 440
    Processing helix  chain 'A' and resid 453 through 464
    Processing helix  chain 'A' and resid 465 through 468
      removed outlier: 3.573A  pdb=" N   GLY A 468 " --> pdb=" O   MET A 465 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 465 through 468'
    Processing helix  chain 'A' and resid 472 through 478
      removed outlier: 3.812A  pdb=" N   LYS A 477 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 496
      removed outlier: 3.604A  pdb=" N   LYS A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 522
    Processing helix  chain 'A' and resid 523 through 528
    Processing helix  chain 'A' and resid 537 through 551
      removed outlier: 4.384A  pdb=" N   LEU A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   HIS A 547 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR A 548 " --> pdb=" O   HIS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 563 through 567
      removed outlier: 5.878A  pdb=" N   ASN A 566 " --> pdb=" O   THR A 563 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 567 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 563 through 567'
    Processing helix  chain 'A' and resid 568 through 577
    Processing helix  chain 'A' and resid 588 through 613
      removed outlier: 4.039A  pdb=" N   ARG A 609 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 648
    Processing helix  chain 'A' and resid 652 through 671
    Processing helix  chain 'A' and resid 683 through 686
    Processing helix  chain 'A' and resid 687 through 699
    Processing helix  chain 'A' and resid 700 through 707
      Proline residue:  A 704  - end of helix
    Processing helix  chain 'A' and resid 708 through 723
      removed outlier: 3.540A  pdb=" N   HIS A 723 " --> pdb=" O   GLU A 719 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
      removed outlier: 8.214A  pdb=" N   VAL A 348 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ILE A 349 " --> pdb=" O   ILE A 357 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 505
      removed outlier: 6.809A  pdb=" N   ALA A 447 " --> pdb=" O   GLN A 503 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   GLY A 505 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE A 449 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ALA A 447 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   MET A 422 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A 449 " --> pdb=" O   MET A 422 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE A 424 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR A 451 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   ASP A 426 " --> pdb=" O   THR A 451 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL A 386 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   GLY A 423 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE A 388 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   MET A 425 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   LYS A 390 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU A 335 " --> pdb=" O   TYR A 387 " (cutoff:3.500A)
      removed outlier: 8.441A  pdb=" N   VAL A 389 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE A 337 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   THR A 267 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ARG A 338 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A 269 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   GLN A 116 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 137
      removed outlier: 3.540A  pdb=" N   ASP A 258 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   HIS A 237 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   THR A 227 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   CYS A 228 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LYS A 232 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   PHE A 216 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   GLY A 221 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 11.966A  pdb=" N   HIS A 318 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 194
      removed outlier: 6.648A  pdb=" N   GLN A 201 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   PHE A 191 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ARG A 199 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   VAL A 193 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   GLN A 197 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA6, first strand: chain 'A' and resid 620 through 621

    289 hydrogen bonds defined for protein.
    834 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: 2.01

  Time building geometry restraints manager: 1.71 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 983
        1.30 -     1.42: 1403
        1.42 -     1.55: 3289
        1.55 -     1.68: 37
        1.68 -     1.81: 52
  Bond restraints: 5764
  Sorted by residual:
  bond pdb=" C   SER A 437 "
       pdb=" O   SER A 437 "
    ideal  model  delta    sigma   weight residual
    1.237  1.169  0.067 1.17e-02 7.31e+03 3.32e+01
  bond pdb=" C   GLU A  49 "
       pdb=" O   GLU A  49 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.29e-02 6.01e+03 1.80e+01
  bond pdb=" CA  ILE A 642 "
       pdb=" CB  ILE A 642 "
    ideal  model  delta    sigma   weight residual
    1.540  1.589 -0.050 1.29e-02 6.01e+03 1.49e+01
  bond pdb=" CA  THR A 209 "
       pdb=" CB  THR A 209 "
    ideal  model  delta    sigma   weight residual
    1.532  1.587 -0.056 1.45e-02 4.76e+03 1.47e+01
  bond pdb=" C   ILE A 642 "
       pdb=" O   ILE A 642 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.039 1.19e-02 7.06e+03 1.05e+01
  ... (remaining 5759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 7510
        1.21 -     2.42: 210
        2.42 -     3.64: 67
        3.64 -     4.85: 18
        4.85 -     6.06: 7
  Bond angle restraints: 7812
  Sorted by residual:
  angle pdb=" N   GLU A  49 "
        pdb=" CA  GLU A  49 "
        pdb=" C   GLU A  49 "
      ideal   model   delta    sigma   weight residual
     112.23  106.86    5.37 1.26e+00 6.30e-01 1.82e+01
  angle pdb=" CA  LEU A 491 "
        pdb=" C   LEU A 491 "
        pdb=" N   SER A 492 "
      ideal   model   delta    sigma   weight residual
     117.63  122.73   -5.10 1.25e+00 6.40e-01 1.66e+01
  angle pdb=" N   ASP A 668 "
        pdb=" CA  ASP A 668 "
        pdb=" C   ASP A 668 "
      ideal   model   delta    sigma   weight residual
     111.07  106.73    4.34 1.07e+00 8.73e-01 1.65e+01
  angle pdb=" N   ILE A 642 "
        pdb=" CA  ILE A 642 "
        pdb=" CB  ILE A 642 "
      ideal   model   delta    sigma   weight residual
     110.58  116.35   -5.77 1.50e+00 4.44e-01 1.48e+01
  angle pdb=" C   ASP A 668 "
        pdb=" CA  ASP A 668 "
        pdb=" CB  ASP A 668 "
      ideal   model   delta    sigma   weight residual
     110.88  104.99    5.89 1.57e+00 4.06e-01 1.41e+01
  ... (remaining 7807 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 3286
       16.84 -    33.68: 168
       33.68 -    50.51: 26
       50.51 -    67.35: 11
       67.35 -    84.19: 8
  Dihedral angle restraints: 3499
    sinusoidal: 1415
      harmonic: 2084
  Sorted by residual:
  dihedral pdb=" CA  LEU A 343 "
           pdb=" C   LEU A 343 "
           pdb=" N   MET A 344 "
           pdb=" CA  MET A 344 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.90  -17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CB  MET A 470 "
           pdb=" CG  MET A 470 "
           pdb=" SD  MET A 470 "
           pdb=" CE  MET A 470 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.11  -49.11     3      1.50e+01 4.44e-03 8.73e+00
  dihedral pdb=" CA  GLN A 186 "
           pdb=" CB  GLN A 186 "
           pdb=" CG  GLN A 186 "
           pdb=" CD  GLN A 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.88   46.12     3      1.50e+01 4.44e-03 8.28e+00
  ... (remaining 3496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 712
       0.050 -    0.100: 108
       0.100 -    0.150: 35
       0.150 -    0.201: 4
       0.201 -    0.251: 5
  Chirality restraints: 864
  Sorted by residual:
  chirality pdb=" CG  LEU A 210 "
            pdb=" CB  LEU A 210 "
            pdb=" CD1 LEU A 210 "
            pdb=" CD2 LEU A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 118 "
            pdb=" CA  VAL A 118 "
            pdb=" CG1 VAL A 118 "
            pdb=" CG2 VAL A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.86    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU A 491 "
            pdb=" CB  LEU A 491 "
            pdb=" CD1 LEU A 491 "
            pdb=" CD2 LEU A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 861 not shown)

  Planarity restraints: 1034
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 197 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.11e+00
        pdb=" C   GLN A 197 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLN A 197 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 198 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 490 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.31e+00
        pdb=" C   VAL A 490 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   VAL A 490 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 491 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 569 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   PHE A 569 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   PHE A 569 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLU A 570 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1031 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1550
        2.82 -     3.34: 5621
        3.34 -     3.86: 9547
        3.86 -     4.38: 11823
        4.38 -     4.90: 20105
  Nonbonded interactions: 48646
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 104 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   PHE A 453 "
            pdb=" OG1 THR A 457 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" OG  SER A 381 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   ASP A 426 "
            pdb=" OH  TYR A 485 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OG1 THR A 451 "
            pdb=" OE1 GLU A 486 "
     model   vdw
     2.349 3.040
  ... (remaining 48641 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:                    0.060
  Process input model:                     18.060
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:14.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
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      :  0.005   0.080   5764  Z= 0.339
  Angle     :  0.581   6.059   7812  Z= 0.361
  Chirality :  0.045   0.251    864
  Planarity :  0.004   0.036   1034
  Dihedral  : 11.882  84.188   2155
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.83 %
    Favored  : 99.00 %
  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: -0.02 (0.31), residues: 721
  helix:  1.12 (0.28), residues: 352
  sheet: -1.77 (0.56), residues: 69
  loop : -0.89 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 544 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.003   0.000   ARG A 636 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  281 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6061 (mm-30)
REVERT: A  570 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6709 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 1.4017
  time to fit residues: 138.5488
Evaluate side-chains
  64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 378 GLN
A 593 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.160166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143186 restraints weight = 5963.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.26
r_work: 0.3588 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5764  Z= 0.351
  Angle     :  0.594   7.478   7812  Z= 0.317
  Chirality :  0.046   0.145    864
  Planarity :  0.005   0.037   1034
  Dihedral  :  4.390  18.173    784
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.50 %
    Favored  : 89.17 %
  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: -0.04 (0.31), residues: 721
  helix:  1.09 (0.28), residues: 355
  sheet: -1.69 (0.57), residues: 69
  loop : -0.93 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 169 
 HIS   0.008   0.001   HIS A 648 
 PHE   0.011   0.002   PHE A 448 
 TYR   0.019   0.002   TYR A 485 
 ARG   0.005   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7388 (ptt90) cc_final: 0.7129 (ptt90)
REVERT: A  281 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6474 (mm-30)
REVERT: A  629 MET cc_start: 0.8436 (ttp) cc_final: 0.8062 (ttt)
REVERT: A  669 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6897 (tt0)
  outliers start: 8
  outliers final: 1
  residues processed: 72
  average time/residue: 1.3412
  time to fit residues: 101.2210
Evaluate side-chains
  66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.159042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.141956 restraints weight = 6120.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.26
r_work: 0.3530 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5764  Z= 0.216
  Angle     :  0.502   6.590   7812  Z= 0.268
  Chirality :  0.042   0.141    864
  Planarity :  0.004   0.037   1034
  Dihedral  :  4.172  17.043    784
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.83 %
    Favored  : 86.50 %
  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:  0.21 (0.31), residues: 721
  helix:  1.33 (0.28), residues: 358
  sheet: -1.72 (0.57), residues: 68
  loop : -0.84 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  36 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.018   0.001   TYR A 485 
 ARG   0.003   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7258 (ptt90) cc_final: 0.7056 (ptt90)
REVERT: A   64 LEU cc_start: 0.7832 (tp) cc_final: 0.7611 (tp)
REVERT: A  281 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6487 (mm-30)
REVERT: A  515 MET cc_start: 0.7652 (mmt) cc_final: 0.7443 (mmp)
REVERT: A  623 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.5151 (tt)
REVERT: A  629 MET cc_start: 0.8361 (ttp) cc_final: 0.8042 (ttt)
REVERT: A  669 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6864 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 77
  average time/residue: 1.1917
  time to fit residues: 96.3580
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.164304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147908 restraints weight = 6053.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.22
r_work: 0.3540 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5764  Z= 0.211
  Angle     :  0.490   6.462   7812  Z= 0.261
  Chirality :  0.042   0.140    864
  Planarity :  0.004   0.036   1034
  Dihedral  :  4.119  16.291    784
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.33 %
    Favored  : 85.00 %
  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:  0.34 (0.31), residues: 721
  helix:  1.45 (0.28), residues: 358
  sheet: -1.56 (0.58), residues: 68
  loop : -0.82 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.003   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.580 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7183 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7452 (m-10) cc_final: 0.6898 (m-80)
REVERT: A  281 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6497 (mm-30)
REVERT: A  623 ILE cc_start: 0.5477 (OUTLIER) cc_final: 0.5127 (tt)
REVERT: A  629 MET cc_start: 0.8325 (ttp) cc_final: 0.8091 (ttt)
REVERT: A  669 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6854 (tt0)
  outliers start: 10
  outliers final: 3
  residues processed: 74
  average time/residue: 1.1464
  time to fit residues: 89.2846
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 63 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.163979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147771 restraints weight = 5984.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.21
r_work: 0.3537 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5764  Z= 0.219
  Angle     :  0.493   6.023   7812  Z= 0.261
  Chirality :  0.042   0.136    864
  Planarity :  0.004   0.036   1034
  Dihedral  :  4.097  16.116    784
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.50 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.31), residues: 721
  helix:  1.45 (0.28), residues: 358
  sheet: -1.35 (0.60), residues: 64
  loop : -0.89 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 636 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7526 (ptp90) cc_final: 0.6827 (ptt90)
REVERT: A   97 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7187 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7457 (m-10) cc_final: 0.6890 (m-80)
REVERT: A  281 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6509 (mm-30)
REVERT: A  550 GLN cc_start: 0.8332 (mt0) cc_final: 0.8114 (mt0)
REVERT: A  623 ILE cc_start: 0.5446 (OUTLIER) cc_final: 0.5084 (tt)
REVERT: A  629 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8086 (ttt)
REVERT: A  669 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6839 (tt0)
  outliers start: 17
  outliers final: 5
  residues processed: 77
  average time/residue: 1.1513
  time to fit residues: 93.3154
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   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 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.159107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.142104 restraints weight = 6151.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.26
r_work: 0.3552 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5764  Z= 0.209
  Angle     :  0.495   8.384   7812  Z= 0.261
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  4.061  15.994    784
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.00 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.31), residues: 721
  helix:  1.54 (0.28), residues: 359
  sheet: -1.39 (0.61), residues: 64
  loop : -0.89 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5337 (mp)
REVERT: A   97 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7185 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7514 (m-10) cc_final: 0.6946 (m-80)
REVERT: A  281 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6519 (mm-30)
REVERT: A  550 GLN cc_start: 0.8325 (mt0) cc_final: 0.8108 (mt0)
REVERT: A  623 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.5067 (tt)
REVERT: A  629 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8081 (ttt)
REVERT: A  669 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6826 (tt0)
  outliers start: 10
  outliers final: 5
  residues processed: 71
  average time/residue: 1.2764
  time to fit residues: 95.0350
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9980
   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 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.166334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.150120 restraints weight = 5963.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.21
r_work: 0.3533 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5764  Z= 0.188
  Angle     :  0.472   5.275   7812  Z= 0.251
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.053   1034
  Dihedral  :  3.991  15.764    784
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.17 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.51 (0.32), residues: 721
  helix:  1.61 (0.28), residues: 360
  sheet: -1.34 (0.61), residues: 64
  loop : -0.84 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.010   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5244 (mp)
REVERT: A   97 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7194 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7458 (m-10) cc_final: 0.6914 (m-80)
REVERT: A  281 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6466 (mm-30)
REVERT: A  550 GLN cc_start: 0.8316 (mt0) cc_final: 0.8100 (mt0)
REVERT: A  623 ILE cc_start: 0.5489 (OUTLIER) cc_final: 0.5095 (tt)
REVERT: A  629 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8030 (ttt)
REVERT: A  669 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6822 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 1.2114
  time to fit residues: 89.2461
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.165160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149195 restraints weight = 5957.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.19
r_work: 0.3566 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5764  Z= 0.192
  Angle     :  0.476   5.283   7812  Z= 0.252
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.037   1034
  Dihedral  :  3.983  16.006    784
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.33 %
    Favored  : 83.50 %
  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:  0.52 (0.32), residues: 721
  helix:  1.63 (0.28), residues: 360
  sheet: -1.30 (0.62), residues: 64
  loop : -0.85 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.010   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 288 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5244 (mp)
REVERT: A   97 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7178 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7464 (m-10) cc_final: 0.6928 (m-80)
REVERT: A  281 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6462 (mm-30)
REVERT: A  550 GLN cc_start: 0.8300 (mt0) cc_final: 0.8086 (mt0)
REVERT: A  623 ILE cc_start: 0.5512 (OUTLIER) cc_final: 0.5116 (tt)
REVERT: A  629 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8033 (ttt)
REVERT: A  669 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6828 (tt0)
  outliers start: 13
  outliers final: 6
  residues processed: 73
  average time/residue: 1.5761
  time to fit residues: 120.9843
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.165076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.149885 restraints weight = 5899.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.12
r_work: 0.3520 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5764  Z= 0.230
  Angle     :  0.497   5.368   7812  Z= 0.263
  Chirality :  0.042   0.135    864
  Planarity :  0.004   0.038   1034
  Dihedral  :  4.068  16.536    784
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.50 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.32), residues: 721
  helix:  1.52 (0.28), residues: 359
  sheet: -1.31 (0.63), residues: 62
  loop : -0.89 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 636 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7222 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7463 (m-10) cc_final: 0.6918 (m-80)
REVERT: A  281 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6479 (mm-30)
REVERT: A  550 GLN cc_start: 0.8320 (mt0) cc_final: 0.8092 (mt0)
REVERT: A  623 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.5169 (tt)
REVERT: A  629 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8011 (ttt)
REVERT: A  669 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6815 (tt0)
  outliers start: 13
  outliers final: 7
  residues processed: 71
  average time/residue: 1.1648
  time to fit residues: 87.0871
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.164608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.148674 restraints weight = 6086.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.19
r_work: 0.3531 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5764  Z= 0.200
  Angle     :  0.501   8.455   7812  Z= 0.261
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.037   1034
  Dihedral  :  4.017  16.370    784
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.67 %
    Favored  : 83.50 %
  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:  0.47 (0.32), residues: 721
  helix:  1.57 (0.28), residues: 359
  sheet: -1.29 (0.63), residues: 62
  loop : -0.86 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 288 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5189 (mp)
REVERT: A   97 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7173 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7434 (m-10) cc_final: 0.6868 (m-80)
REVERT: A  281 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6448 (mm-30)
REVERT: A  486 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7282 (mm-30)
REVERT: A  550 GLN cc_start: 0.8310 (mt0) cc_final: 0.8059 (mt0)
REVERT: A  623 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5123 (tt)
REVERT: A  629 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8040 (ttt)
REVERT: A  669 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6831 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 70
  average time/residue: 1.5616
  time to fit residues: 115.3485
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 68 optimal weight:    0.4980
   chunk 65 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.149727 restraints weight = 6025.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.22
r_work: 0.3561 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5764  Z= 0.202
  Angle     :  0.492   7.406   7812  Z= 0.259
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  4.021  16.490    784
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.83 %
    Favored  : 83.50 %
  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:  0.47 (0.32), residues: 721
  helix:  1.57 (0.28), residues: 359
  sheet: -1.30 (0.64), residues: 62
  loop : -0.85 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 636 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3864.86 seconds
wall clock time: 67 minutes 34.75 seconds (4054.75 seconds total)