Starting phenix.real_space_refine
on Fri Aug 22 16:14:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yqm_34029/08_2025/7yqm_34029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yqm_34029/08_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_34029/08_2025/7yqm_34029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yqm_34029/08_2025/7yqm_34029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yqm_34029/08_2025/7yqm_34029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yqm_34029/08_2025/7yqm_34029.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.29, per 1000 atoms: 0.23
  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: 0.45
  Conformation dependent library (CDL) restraints added in 300.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.19
  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: 0.77

  Time building geometry restraints manager: 0.60 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.100
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:5.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.060
-------------------------------------------------------------------------------
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= 0.291
  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 : 1.69
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.000   ARG A 636 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.008   0.001   PHE A 191 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 5764)
  covalent geometry    : angle       0.58087 ( 7812)
  hydrogen bonds       : bond        0.14316 (  289)
  hydrogen bonds       : angle       6.07057 (  834)

*********************** 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  : 0.190 
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: 0.6048
  time to fit residues: 59.6040
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  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.168630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152305 restraints weight = 5929.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.22
r_work: 0.3607 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5764  Z= 0.116
  Angle     :  0.493   5.951   7812  Z= 0.265
  Chirality :  0.041   0.138    864
  Planarity :  0.004   0.038   1034
  Dihedral  :  3.991  15.546    784
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  9.33 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.32), residues: 721
  helix:  1.54 (0.28), residues: 357
  sheet: -1.68 (0.60), residues: 62
  loop : -0.55 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 527 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.008   0.001   PHE A 448 
 TRP   0.007   0.001   TRP A 350 
 HIS   0.004   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5764)
  covalent geometry    : angle       0.49252 ( 7812)
  hydrogen bonds       : bond        0.04069 (  289)
  hydrogen bonds       : angle       4.93385 (  834)

*********************** 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: 4
    poor density    : 72
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  281 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6431 (mm-30)
REVERT: A  312 LYS cc_start: 0.5859 (ttmt) cc_final: 0.5513 (mtpp)
REVERT: A  629 MET cc_start: 0.8346 (ttp) cc_final: 0.8007 (ttt)
  outliers start: 4
  outliers final: 0
  residues processed: 74
  average time/residue: 0.5638
  time to fit residues: 43.5053
Evaluate side-chains
  66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.161451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.144586 restraints weight = 6036.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.24
r_work: 0.3565 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   5764  Z= 0.222
  Angle     :  0.584   6.893   7812  Z= 0.311
  Chirality :  0.046   0.143    864
  Planarity :  0.005   0.039   1034
  Dihedral  :  4.389  17.531    784
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.00 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.31), residues: 721
  helix:  1.17 (0.28), residues: 355
  sheet: -1.73 (0.56), residues: 70
  loop : -0.99 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 636 
 TYR   0.019   0.002   TYR A 485 
 PHE   0.010   0.002   PHE A 448 
 TRP   0.011   0.002   TRP A 169 
 HIS   0.008   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 5764)
  covalent geometry    : angle       0.58373 ( 7812)
  hydrogen bonds       : bond        0.05224 (  289)
  hydrogen bonds       : angle       5.10979 (  834)

*********************** 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
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  281 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6505 (mm-30)
REVERT: A  624 HIS cc_start: 0.7533 (m170) cc_final: 0.7238 (m-70)
REVERT: A  629 MET cc_start: 0.8386 (ttp) cc_final: 0.8025 (ttt)
REVERT: A  669 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6914 (tt0)
  outliers start: 12
  outliers final: 3
  residues processed: 71
  average time/residue: 0.5803
  time to fit residues: 43.0939
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  : 0.181 
-------------------------------------------------------------------------------
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  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 44 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.162953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146591 restraints weight = 6015.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.21
r_work: 0.3541 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5764  Z= 0.164
  Angle     :  0.521   6.139   7812  Z= 0.277
  Chirality :  0.043   0.139    864
  Planarity :  0.004   0.038   1034
  Dihedral  :  4.252  16.882    784
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.50 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.31), residues: 721
  helix:  1.26 (0.28), residues: 357
  sheet: -1.65 (0.57), residues: 68
  loop : -0.95 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.018   0.001   TYR A 485 
 PHE   0.009   0.001   PHE A 495 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5764)
  covalent geometry    : angle       0.52118 ( 7812)
  hydrogen bonds       : bond        0.04546 (  289)
  hydrogen bonds       : angle       4.91519 (  834)

*********************** 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
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7507 (ptt180) cc_final: 0.7119 (ptt90)
REVERT: A   97 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7194 (ttp-110)
REVERT: A  281 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6498 (mm-30)
REVERT: A  515 MET cc_start: 0.7819 (mmt) cc_final: 0.7482 (mmp)
REVERT: A  623 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5209 (tt)
REVERT: A  629 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8106 (ttt)
REVERT: A  669 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6853 (tt0)
  outliers start: 11
  outliers final: 3
  residues processed: 77
  average time/residue: 0.5852
  time to fit residues: 47.0749
Evaluate side-chains
  75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  629 MET
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 44 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    0.1980
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.165067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.148967 restraints weight = 6049.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.20
r_work: 0.3523 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1839

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= 0.119
  Angle     :  0.472   5.462   7812  Z= 0.252
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  4.065  15.871    784
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.33 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.31), residues: 721
  helix:  1.52 (0.28), residues: 358
  sheet: -1.39 (0.62), residues: 62
  loop : -0.88 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 527 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.010   0.001   PHE A 495 
 TRP   0.006   0.001   TRP A 481 
 HIS   0.004   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 5764)
  covalent geometry    : angle       0.47216 ( 7812)
  hydrogen bonds       : bond        0.03966 (  289)
  hydrogen bonds       : angle       4.70559 (  834)

*********************** 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
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7088 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7393 (m-10) cc_final: 0.6820 (m-80)
REVERT: A  281 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6418 (mm-30)
REVERT: A  515 MET cc_start: 0.7748 (mmt) cc_final: 0.7457 (mmp)
REVERT: A  623 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5123 (tt)
REVERT: A  629 MET cc_start: 0.8322 (ttp) cc_final: 0.8063 (ttt)
REVERT: A  669 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6807 (tt0)
  outliers start: 11
  outliers final: 3
  residues processed: 77
  average time/residue: 0.5277
  time to fit residues: 42.6488
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
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  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 22 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.1482

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.163268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.147835 restraints weight = 6034.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.12
r_work: 0.3497 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5764  Z= 0.189
  Angle     :  0.542   5.939   7812  Z= 0.288
  Chirality :  0.044   0.139    864
  Planarity :  0.004   0.038   1034
  Dihedral  :  4.264  16.799    784
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.31), residues: 721
  helix:  1.29 (0.28), residues: 357
  sheet: -1.52 (0.57), residues: 70
  loop : -1.00 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 716 
 TYR   0.018   0.002   TYR A 485 
 PHE   0.009   0.002   PHE A 495 
 TRP   0.010   0.002   TRP A 169 
 HIS   0.006   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 5764)
  covalent geometry    : angle       0.54220 ( 7812)
  hydrogen bonds       : bond        0.04748 (  289)
  hydrogen bonds       : angle       4.85786 (  834)

*********************** 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
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7160 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7475 (m-10) cc_final: 0.6916 (m-80)
REVERT: A  206 LYS cc_start: 0.6764 (mmmt) cc_final: 0.6511 (mmpt)
REVERT: A  281 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6518 (mm-30)
REVERT: A  623 ILE cc_start: 0.5526 (OUTLIER) cc_final: 0.5138 (tt)
REVERT: A  629 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8071 (ttt)
REVERT: A  669 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6835 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 75
  average time/residue: 0.5812
  time to fit residues: 45.6285
Evaluate side-chains
  79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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 41 optimal weight:    0.0060
   chunk 65 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 54 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.166195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.149784 restraints weight = 6078.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.24
r_work: 0.3536 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5764  Z= 0.107
  Angle     :  0.463   5.238   7812  Z= 0.247
  Chirality :  0.040   0.135    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  3.972  15.738    784
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.33 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.31), residues: 721
  helix:  1.57 (0.28), residues: 360
  sheet: -1.01 (0.66), residues: 57
  loop : -0.91 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 636 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.010   0.001   PHE A 495 
 TRP   0.006   0.001   TRP A 481 
 HIS   0.003   0.001   HIS A 462 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5764)
  covalent geometry    : angle       0.46270 ( 7812)
  hydrogen bonds       : bond        0.03791 (  289)
  hydrogen bonds       : angle       4.58362 (  834)

*********************** 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
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  126 TYR cc_start: 0.7425 (m-10) cc_final: 0.6853 (m-80)
REVERT: A  281 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6444 (mm-30)
REVERT: A  515 MET cc_start: 0.7722 (mmt) cc_final: 0.7473 (mmp)
REVERT: A  623 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5144 (tt)
REVERT: A  629 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8053 (ttt)
REVERT: A  669 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6819 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 73
  average time/residue: 0.5722
  time to fit residues: 43.7041
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    0.0470
   chunk 71 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.167334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.151154 restraints weight = 5922.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.21
r_work: 0.3548 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5764  Z= 0.118
  Angle     :  0.473   5.247   7812  Z= 0.251
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  3.962  15.779    784
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.50 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.32), residues: 721
  helix:  1.65 (0.28), residues: 360
  sheet: -1.33 (0.62), residues: 64
  loop : -0.81 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 636 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.010   0.001   PHE A 495 
 TRP   0.007   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5764)
  covalent geometry    : angle       0.47315 ( 7812)
  hydrogen bonds       : bond        0.03911 (  289)
  hydrogen bonds       : angle       4.56287 (  834)

*********************** 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
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7420 (ptp90) cc_final: 0.7207 (ptt180)
REVERT: A  126 TYR cc_start: 0.7455 (m-10) cc_final: 0.6903 (m-80)
REVERT: A  281 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6457 (mm-30)
REVERT: A  486 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A  515 MET cc_start: 0.7725 (mmt) cc_final: 0.7448 (mmp)
REVERT: A  623 ILE cc_start: 0.5485 (OUTLIER) cc_final: 0.5101 (tt)
REVERT: A  629 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (ttt)
REVERT: A  669 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6792 (tt0)
  outliers start: 11
  outliers final: 4
  residues processed: 72
  average time/residue: 0.5982
  time to fit residues: 45.0486
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.167043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151120 restraints weight = 6015.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.20
r_work: 0.3563 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5764  Z= 0.106
  Angle     :  0.463   5.201   7812  Z= 0.245
  Chirality :  0.041   0.134    864
  Planarity :  0.004   0.034   1034
  Dihedral  :  3.893  15.847    784
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.83 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.32), residues: 721
  helix:  1.71 (0.28), residues: 361
  sheet: -1.18 (0.63), residues: 63
  loop : -0.74 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 636 
 TYR   0.017   0.001   TYR A 707 
 PHE   0.010   0.001   PHE A 495 
 TRP   0.006   0.001   TRP A 481 
 HIS   0.003   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5764)
  covalent geometry    : angle       0.46261 ( 7812)
  hydrogen bonds       : bond        0.03734 (  289)
  hydrogen bonds       : angle       4.48671 (  834)

*********************** 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: 10
    poor density    : 68
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  126 TYR cc_start: 0.7453 (m-10) cc_final: 0.6949 (m-80)
REVERT: A  281 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6462 (mm-30)
REVERT: A  486 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7544 (mm-30)
REVERT: A  623 ILE cc_start: 0.5484 (OUTLIER) cc_final: 0.5137 (tt)
REVERT: A  629 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7980 (ttt)
REVERT: A  669 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6843 (tt0)
  outliers start: 10
  outliers final: 4
  residues processed: 73
  average time/residue: 0.6314
  time to fit residues: 48.1593
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.164076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.148760 restraints weight = 6018.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.12
r_work: 0.3519 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5764  Z= 0.187
  Angle     :  0.556   7.204   7812  Z= 0.290
  Chirality :  0.044   0.139    864
  Planarity :  0.004   0.036   1034
  Dihedral  :  4.196  16.933    784
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.00 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.31), residues: 721
  helix:  1.43 (0.28), residues: 359
  sheet: -1.28 (0.63), residues: 62
  loop : -0.92 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 636 
 TYR   0.017   0.002   TYR A 485 
 PHE   0.012   0.002   PHE A 453 
 TRP   0.011   0.002   TRP A 169 
 HIS   0.006   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5764)
  covalent geometry    : angle       0.55583 ( 7812)
  hydrogen bonds       : bond        0.04679 (  289)
  hydrogen bonds       : angle       4.76546 (  834)

********************** 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
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7356 (ptp90) cc_final: 0.7109 (ptt180)
REVERT: A   12 ILE cc_start: 0.6198 (OUTLIER) cc_final: 0.5200 (mp)
REVERT: A  126 TYR cc_start: 0.7519 (m-10) cc_final: 0.6957 (m-80)
REVERT: A  281 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6539 (mm-30)
REVERT: A  623 ILE cc_start: 0.5538 (OUTLIER) cc_final: 0.5153 (tt)
REVERT: A  629 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7979 (ttt)
REVERT: A  669 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6916 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 73
  average time/residue: 0.6112
  time to fit residues: 46.6249
Evaluate side-chains
  72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   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 = 0.3891 r_free = 0.3891 target = 0.165857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.150795 restraints weight = 5897.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.11
r_work: 0.3544 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5764  Z= 0.135
  Angle     :  0.504   7.118   7812  Z= 0.265
  Chirality :  0.042   0.137    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  4.085  16.675    784
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.00 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.31), residues: 721
  helix:  1.49 (0.28), residues: 358
  sheet: -1.42 (0.68), residues: 55
  loop : -0.87 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 716 
 TYR   0.017   0.001   TYR A 485 
 PHE   0.009   0.001   PHE A 495 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5764)
  covalent geometry    : angle       0.50397 ( 7812)
  hydrogen bonds       : bond        0.04155 (  289)
  hydrogen bonds       : angle       4.64917 (  834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1864.19 seconds
wall clock time: 32 minutes 29.84 seconds (1949.84 seconds total)