Starting phenix.real_space_refine
on Tue Mar  3 14:08:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nvh_12604/03_2026/7nvh_12604.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.067
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      27      5.16       5
     C    3605      2.51       5
     N     913      2.21       5
     O     983      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5528
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5459
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 717, 5440
          Classifications: {'peptide': 717}
          Link IDs: {'PTRANS': 35, 'TRANS': 681}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 717, 5440
          Classifications: {'peptide': 717}
          Link IDs: {'PTRANS': 35, 'TRANS': 681}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 5532
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.57, per 1000 atoms: 0.46
  Number of scatterers: 5528
  At special positions: 0
  Unit cell: (82.368, 72.384, 106.496, 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      27     16.00
     O     983      8.00
     N     913      7.00
     C    3605      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: 0.68
  Conformation dependent library (CDL) restraints added in 386.9 milliseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1308

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 3 sheets defined
      71.1% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
      removed outlier: 4.100A  pdb=" N   ARG A   7 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   TYR A  10 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG A  11 " --> pdb=" O   ARG A   7 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A  12 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 26
    Processing helix  chain 'A' and resid 30 through 32
      No H-bonds generated for 'chain 'A' and resid 30 through 32'
    Processing helix  chain 'A' and resid 33 through 37
      removed outlier: 3.752A  pdb=" N   HIS A  37 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 33 through 37'
    Processing helix  chain 'A' and resid 48 through 62
    Processing helix  chain 'A' and resid 83 through 95
    Processing helix  chain 'A' and resid 117 through 121
      removed outlier: 3.699A  pdb=" N   ALA A 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 148
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 165 through 175
    Processing helix  chain 'A' and resid 175 through 201
      removed outlier: 3.821A  pdb=" N   THR A 179 " --> pdb=" O   GLY A 175 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   LEU A 189 " --> pdb=" O   GLU A 185 " (cutoff:3.500A)
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'A' and resid 202 through 228
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 247 through 266
      removed outlier: 3.707A  pdb=" N   GLY A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 298
      removed outlier: 4.167A  pdb=" N   ARG A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   GLY A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 302
    Processing helix  chain 'A' and resid 304 through 337
      removed outlier: 3.667A  pdb=" N   TYR A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      Proline residue:  A 330  - end of helix
    Processing helix  chain 'A' and resid 338 through 341
      removed outlier: 4.187A  pdb=" N   ASP A 341 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 338 through 341'
    Processing helix  chain 'A' and resid 384 through 392
      removed outlier: 3.669A  pdb=" N   VAL A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG A 391 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 409
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 423 through 427
      removed outlier: 3.633A  pdb=" N   LEU A 427 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 444
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.904A  pdb=" N   ASN A 491 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 519
      No H-bonds generated for 'chain 'A' and resid 517 through 519'
    Processing helix  chain 'A' and resid 520 through 529
      removed outlier: 3.708A  pdb=" N   THR A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A 527 " --> pdb=" O   LYS A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
      removed outlier: 3.510A  pdb=" N   LEU A 549 " --> pdb=" O   PRO A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 578
      removed outlier: 3.876A  pdb=" N   VAL A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 607
      removed outlier: 3.691A  pdb=" N   ILE A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 616
    Processing helix  chain 'A' and resid 623 through 655
      removed outlier: 4.205A  pdb=" N   ARG A 648 " --> pdb=" O   PHE A 644 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   MET A 649 " --> pdb=" O   LEU A 645 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG A 655 " --> pdb=" O   GLU A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 670
      removed outlier: 3.780A  pdb=" N   THR A 670 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 690
      removed outlier: 3.620A  pdb=" N   PHE A 688 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE A 690 " --> pdb=" O   GLY A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 713
    Processing helix  chain 'A' and resid 713 through 727
      removed outlier: 4.629A  pdb=" N   VAL A 719 " --> pdb=" O   ARG A 715 " (cutoff:3.500A)
      Proline residue:  A 720  - end of helix
    Processing helix  chain 'A' and resid 728 through 732
      removed outlier: 3.735A  pdb=" N   TRP A 731 " --> pdb=" O   ASP A 728 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP A 732 " --> pdb=" O   ASP A 729 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 728 through 732'
    Processing helix  chain 'A' and resid 734 through 744
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110
    Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 495

    341 hydrogen bonds defined for protein.
    979 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 868
        1.32 -     1.44: 1423
        1.44 -     1.56: 3298
        1.56 -     1.68: 11
        1.68 -     1.81: 50
  Bond restraints: 5650
  Sorted by residual:
  bond pdb=" CCS AV0 A 801 "
       pdb=" OBZ AV0 A 801 "
    ideal  model  delta    sigma   weight residual
    1.392  1.480 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C1  AV0 A 801 "
       pdb=" O5  AV0 A 801 "
    ideal  model  delta    sigma   weight residual
    1.403  1.483 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" CCR AV0 A 801 "
       pdb=" OBY AV0 A 801 "
    ideal  model  delta    sigma   weight residual
    1.392  1.471 -0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" CBT AV0 A 801 "
       pdb=" CCM AV0 A 801 "
    ideal  model  delta    sigma   weight residual
    1.528  1.606 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" CCJ AV0 A 801 "
       pdb=" OBX AV0 A 801 "
    ideal  model  delta    sigma   weight residual
    1.403  1.474 -0.071 2.00e-02 2.50e+03 1.28e+01
  ... (remaining 5645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 7481
        1.83 -     3.67: 151
        3.67 -     5.50: 54
        5.50 -     7.33: 5
        7.33 -     9.16: 2
  Bond angle restraints: 7693
  Sorted by residual:
  angle pdb=" N   ASP A 640 "
        pdb=" CA  ASP A 640 "
        pdb=" C   ASP A 640 "
      ideal   model   delta    sigma   weight residual
     111.07  107.04    4.03 1.07e+00 8.73e-01 1.42e+01
  angle pdb=" N   ASN A 390 "
        pdb=" CA  ASN A 390 "
        pdb=" C   ASN A 390 "
      ideal   model   delta    sigma   weight residual
     114.75  110.33    4.42 1.26e+00 6.30e-01 1.23e+01
  angle pdb=" C4  AV0 A 801 "
        pdb=" O4  AV0 A 801 "
        pdb=" CCR AV0 A 801 "
      ideal   model   delta    sigma   weight residual
     119.55  110.89    8.66 3.00e+00 1.11e-01 8.33e+00
  angle pdb=" CA  TYR A 698 "
        pdb=" CB  TYR A 698 "
        pdb=" CG  TYR A 698 "
      ideal   model   delta    sigma   weight residual
     113.90  119.02   -5.12 1.80e+00 3.09e-01 8.09e+00
  angle pdb=" C   ASP A 710 "
        pdb=" CA  ASP A 710 "
        pdb=" CB  ASP A 710 "
      ideal   model   delta    sigma   weight residual
     110.31  104.45    5.86 2.09e+00 2.29e-01 7.85e+00
  ... (remaining 7688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.30: 3335
       35.30 -    70.60: 73
       70.60 -   105.90: 12
      105.90 -   141.20: 10
      141.20 -   176.50: 2
  Dihedral angle restraints: 3432
    sinusoidal: 1387
      harmonic: 2045
  Sorted by residual:
  dihedral pdb=" CA  LEU A  94 "
           pdb=" C   LEU A  94 "
           pdb=" N   ASN A  95 "
           pdb=" CA  ASN A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.12   25.88     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  VAL A 389 "
           pdb=" C   VAL A 389 "
           pdb=" N   ASN A 390 "
           pdb=" CA  ASN A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.18   24.82     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CCF AV0 A 801 "
           pdb=" CCQ AV0 A 801 "
           pdb=" OCB AV0 A 801 "
           pdb=" CCS AV0 A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -112.55   63.95 -176.50     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 650
       0.044 -    0.088: 215
       0.088 -    0.132: 53
       0.132 -    0.176: 10
       0.176 -    0.220: 2
  Chirality restraints: 930
  Sorted by residual:
  chirality pdb=" CCS AV0 A 801 "
            pdb=" CCW AV0 A 801 "
            pdb=" OBZ AV0 A 801 "
            pdb=" OCB AV0 A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    2.46   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CCQ AV0 A 801 "
            pdb=" CCF AV0 A 801 "
            pdb=" CCH AV0 A 801 "
            pdb=" OCB AV0 A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.34    0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  GLN A 238 "
            pdb=" N   GLN A 238 "
            pdb=" C   GLN A 238 "
            pdb=" CB  GLN A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.70e-01
  ... (remaining 927 not shown)

  Planarity restraints: 950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  83 "   -0.035 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO A  84 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A  84 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  84 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  75 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO A  76 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 583 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO A 584 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 584 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 584 "    0.027 5.00e-02 4.00e+02
  ... (remaining 947 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 105
        2.70 -     3.25: 5551
        3.25 -     3.80: 8793
        3.80 -     4.35: 11660
        4.35 -     4.90: 19780
  Nonbonded interactions: 45889
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 323 "
            pdb=" OG1 THR A 327 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" OG1 THR A 659 "
            pdb=" OD1 ASP A 728 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" OE2 GLU A 495 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER A  66 "
            pdb=" OG  SER A 131 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NH2 ARG A  65 "
            pdb=" O   GLY A 136 "
     model   vdw
     2.327 3.120
  ... (remaining 45884 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=0.50 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:             2.750
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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      :  0.006   0.088   5650  Z= 0.300
  Angle     :  0.726   9.163   7693  Z= 0.374
  Chirality :  0.046   0.220    930
  Planarity :  0.005   0.054    950
  Dihedral  : 18.545 176.503   2124
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  0.17 %
    Favored  : 99.13 %
  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 are not related in a simple way.
  whole: -0.42 (0.33), residues: 716
  helix:  0.17 (0.25), residues: 479
  sheet: -0.78 (0.86), residues: 38
  loop : -0.98 (0.46), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  96 
 TYR   0.022   0.001   TYR A 698 
 PHE   0.011   0.001   PHE A 306 
 TRP   0.012   0.001   TRP A 736 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 5650)
  covalent geometry    : angle       0.72610 ( 7693)
  hydrogen bonds       : bond        0.15882 (  341)
  hydrogen bonds       : angle       6.22003 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8401 (tp) cc_final: 0.8018 (pp)
REVERT: A  562 MET cc_start: 0.7830 (tmm) cc_final: 0.7599 (tmt)
REVERT: A  710 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7737 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.4798
  time to fit residues: 33.3802
Evaluate side-chains
  59 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  710 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.109560 restraints weight = 19792.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.89
r_work: 0.3144 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5650  Z= 0.144
  Angle     :  0.655   8.545   7693  Z= 0.323
  Chirality :  0.044   0.239    930
  Planarity :  0.005   0.048    950
  Dihedral  : 16.228 177.111    899
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  4.50 %
    Favored  : 93.60 %
  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 are not related in a simple way.
  whole: -0.05 (0.33), residues: 716
  helix:  0.45 (0.25), residues: 487
  sheet: -0.58 (0.88), residues: 38
  loop : -0.91 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.025   0.001   TYR A 698 
 PHE   0.009   0.001   PHE A 306 
 TRP   0.010   0.001   TRP A 736 
 HIS   0.002   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5650)
  covalent geometry    : angle       0.65478 ( 7693)
  hydrogen bonds       : bond        0.03975 (  341)
  hydrogen bonds       : angle       4.70310 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8573 (tp) cc_final: 0.8207 (pp)
REVERT: A  710 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8178 (t70)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 0.5158
  time to fit residues: 34.0447
Evaluate side-chains
  63 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  704 MET
Chi-restraints excluded: chain A residue  710 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0050
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0040
   overall best weight:    0.4606

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 181 GLN
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.126660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114102 restraints weight = 12062.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.20
r_work: 0.3221 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5650  Z= 0.120
  Angle     :  0.596   9.134   7693  Z= 0.293
  Chirality :  0.041   0.176    930
  Planarity :  0.005   0.046    950
  Dihedral  : 12.855 174.689    899
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  6.92 %
    Favored  : 91.35 %
  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 are not related in a simple way.
  whole:  0.27 (0.33), residues: 716
  helix:  0.71 (0.25), residues: 490
  sheet: -0.31 (0.87), residues: 38
  loop : -0.93 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.024   0.001   TYR A 698 
 PHE   0.009   0.001   PHE A 306 
 TRP   0.010   0.001   TRP A 736 
 HIS   0.006   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5650)
  covalent geometry    : angle       0.59552 ( 7693)
  hydrogen bonds       : bond        0.03527 (  341)
  hydrogen bonds       : angle       4.44601 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8196 (ptpp)
REVERT: A  406 ILE cc_start: 0.8621 (tp) cc_final: 0.8284 (pp)
  outliers start: 8
  outliers final: 3
  residues processed: 68
  average time/residue: 0.5234
  time to fit residues: 37.4750
Evaluate side-chains
  64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  704 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.110724 restraints weight = 14955.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.47
r_work: 0.3144 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5650  Z= 0.183
  Angle     :  0.617   9.260   7693  Z= 0.308
  Chirality :  0.043   0.191    930
  Planarity :  0.005   0.045    950
  Dihedral  : 12.525 176.186    897
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  8.48 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.33), residues: 716
  helix:  0.66 (0.24), residues: 494
  sheet: -0.12 (0.80), residues: 44
  loop : -0.69 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.024   0.001   TYR A 698 
 PHE   0.024   0.001   PHE A 575 
 TRP   0.007   0.001   TRP A 493 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 5650)
  covalent geometry    : angle       0.61748 ( 7693)
  hydrogen bonds       : bond        0.03675 (  341)
  hydrogen bonds       : angle       4.48189 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8159 (ptpp)
REVERT: A  406 ILE cc_start: 0.8556 (tp) cc_final: 0.8204 (pp)
  outliers start: 10
  outliers final: 5
  residues processed: 67
  average time/residue: 0.6291
  time to fit residues: 44.1194
Evaluate side-chains
  67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  491 ASN
Chi-restraints excluded: chain A residue  704 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   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 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.110160 restraints weight = 17266.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.59
r_work: 0.3150 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5650  Z= 0.149
  Angle     :  0.596  10.023   7693  Z= 0.296
  Chirality :  0.041   0.165    930
  Planarity :  0.005   0.045    950
  Dihedral  : 12.494 176.604    897
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.73 %
    Favored  : 87.72 %
  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 are not related in a simple way.
  whole:  0.33 (0.33), residues: 716
  helix:  0.76 (0.24), residues: 493
  sheet: -0.01 (0.87), residues: 38
  loop : -1.00 (0.49), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 738 
 TYR   0.026   0.001   TYR A 698 
 PHE   0.017   0.001   PHE A 575 
 TRP   0.008   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5650)
  covalent geometry    : angle       0.59644 ( 7693)
  hydrogen bonds       : bond        0.03446 (  341)
  hydrogen bonds       : angle       4.42305 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8426 (ptmt) cc_final: 0.8174 (ptpp)
REVERT: A  406 ILE cc_start: 0.8560 (tp) cc_final: 0.8213 (pp)
  outliers start: 7
  outliers final: 3
  residues processed: 66
  average time/residue: 0.5487
  time to fit residues: 38.0416
Evaluate side-chains
  65 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0770
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0270
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.125635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.113357 restraints weight = 12124.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.16
r_work: 0.3182 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5650  Z= 0.111
  Angle     :  0.575  11.549   7693  Z= 0.280
  Chirality :  0.040   0.154    930
  Planarity :  0.005   0.045    950
  Dihedral  : 12.402 178.009    897
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.59 %
    Favored  : 86.68 %
  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 are not related in a simple way.
  whole:  0.68 (0.33), residues: 716
  helix:  1.01 (0.25), residues: 490
  sheet:  0.15 (0.86), residues: 38
  loop : -0.82 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 738 
 TYR   0.021   0.001   TYR A 698 
 PHE   0.015   0.001   PHE A 575 
 TRP   0.010   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5650)
  covalent geometry    : angle       0.57470 ( 7693)
  hydrogen bonds       : bond        0.03150 (  341)
  hydrogen bonds       : angle       4.30912 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8494 (ptmt) cc_final: 0.8270 (ptpp)
REVERT: A   96 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6986 (mtp-110)
REVERT: A  406 ILE cc_start: 0.8585 (tp) cc_final: 0.8251 (pp)
REVERT: A  696 MET cc_start: 0.8949 (tpp) cc_final: 0.8654 (mmm)
REVERT: A  738 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7455 (tpp-160)
  outliers start: 8
  outliers final: 2
  residues processed: 71
  average time/residue: 0.5915
  time to fit residues: 43.9675
Evaluate side-chains
  65 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  704 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0770
   chunk 56 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0010
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   overall best weight:    0.3542

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.127826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.114756 restraints weight = 14667.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.44
r_work: 0.3217 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5650  Z= 0.108
  Angle     :  0.580  14.406   7693  Z= 0.278
  Chirality :  0.040   0.158    930
  Planarity :  0.005   0.044    950
  Dihedral  : 12.285 178.934    897
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.11 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.33), residues: 716
  helix:  1.14 (0.25), residues: 490
  sheet:  0.29 (0.87), residues: 38
  loop : -0.83 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 738 
 TYR   0.024   0.001   TYR A 698 
 PHE   0.014   0.001   PHE A 575 
 TRP   0.009   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5650)
  covalent geometry    : angle       0.57958 ( 7693)
  hydrogen bonds       : bond        0.03074 (  341)
  hydrogen bonds       : angle       4.28658 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8165 (ptpp)
REVERT: A  406 ILE cc_start: 0.8476 (tp) cc_final: 0.8154 (pp)
REVERT: A  738 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7306 (tpp-160)
  outliers start: 7
  outliers final: 1
  residues processed: 68
  average time/residue: 0.6288
  time to fit residues: 44.6487
Evaluate side-chains
  64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue  116 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 616 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.111618 restraints weight = 14696.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.41
r_work: 0.3201 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5650  Z= 0.146
  Angle     :  0.603  12.712   7693  Z= 0.292
  Chirality :  0.041   0.166    930
  Planarity :  0.005   0.052    950
  Dihedral  : 12.175 179.293    897
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 12.98 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.33), residues: 716
  helix:  1.09 (0.25), residues: 491
  sheet:  0.38 (0.89), residues: 38
  loop : -0.75 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  96 
 TYR   0.024   0.001   TYR A 698 
 PHE   0.012   0.001   PHE A 575 
 TRP   0.006   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5650)
  covalent geometry    : angle       0.60267 ( 7693)
  hydrogen bonds       : bond        0.03273 (  341)
  hydrogen bonds       : angle       4.30704 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8375 (ptmt) cc_final: 0.8171 (ptpp)
REVERT: A  406 ILE cc_start: 0.8477 (tp) cc_final: 0.8155 (pp)
REVERT: A  738 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7383 (tpp-160)
  outliers start: 2
  outliers final: 1
  residues processed: 64
  average time/residue: 0.6115
  time to fit residues: 40.9143
Evaluate side-chains
  61 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0000
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.110691 restraints weight = 22764.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.04
r_work: 0.3158 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5650  Z= 0.132
  Angle     :  0.607  12.842   7693  Z= 0.291
  Chirality :  0.041   0.161    930
  Planarity :  0.005   0.053    950
  Dihedral  : 12.040 179.853    897
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.98 %
    Favored  : 85.99 %
  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 are not related in a simple way.
  whole:  0.79 (0.33), residues: 716
  helix:  1.08 (0.25), residues: 494
  sheet:  0.39 (0.89), residues: 38
  loop : -0.78 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  96 
 TYR   0.022   0.001   TYR A 698 
 PHE   0.011   0.001   PHE A 575 
 TRP   0.007   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5650)
  covalent geometry    : angle       0.60705 ( 7693)
  hydrogen bonds       : bond        0.03209 (  341)
  hydrogen bonds       : angle       4.29254 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8199 (ptpp)
REVERT: A  406 ILE cc_start: 0.8521 (tp) cc_final: 0.8192 (pp)
REVERT: A  696 MET cc_start: 0.8782 (tpp) cc_final: 0.8318 (tmm)
REVERT: A  738 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7397 (tpp-160)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.5498
  time to fit residues: 36.9198
Evaluate side-chains
  64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  630 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0000
   chunk 43 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0470
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4082

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.112602 restraints weight = 19529.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.88
r_work: 0.3173 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5650  Z= 0.112
  Angle     :  0.602  13.224   7693  Z= 0.284
  Chirality :  0.040   0.163    930
  Planarity :  0.005   0.052    950
  Dihedral  : 11.764 179.918    897
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 14.01 %
    Favored  : 85.29 %
  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 are not related in a simple way.
  whole:  0.98 (0.33), residues: 716
  helix:  1.19 (0.25), residues: 492
  sheet:  0.39 (0.88), residues: 38
  loop : -0.59 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  96 
 TYR   0.022   0.001   TYR A 698 
 PHE   0.012   0.001   PHE A 575 
 TRP   0.009   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5650)
  covalent geometry    : angle       0.60192 ( 7693)
  hydrogen bonds       : bond        0.03069 (  341)
  hydrogen bonds       : angle       4.22316 (  979)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.8418 (ptmt) cc_final: 0.8201 (ptpp)
REVERT: A   96 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.6612 (ttt-90)
REVERT: A  406 ILE cc_start: 0.8485 (tp) cc_final: 0.8162 (pp)
REVERT: A  696 MET cc_start: 0.8774 (tpp) cc_final: 0.8371 (tmm)
REVERT: A  738 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7306 (tpp-160)
  outliers start: 2
  outliers final: 2
  residues processed: 69
  average time/residue: 0.5499
  time to fit residues: 39.8621
Evaluate side-chains
  65 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  630 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0670
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0050
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0570
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.3250

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 616 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.127323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.114424 restraints weight = 14813.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.44
r_work: 0.3215 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5650  Z= 0.107
  Angle     :  0.594  14.930   7693  Z= 0.280
  Chirality :  0.040   0.170    930
  Planarity :  0.005   0.051    950
  Dihedral  : 11.477 177.745    897
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 14.01 %
    Favored  : 85.29 %
  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 are not related in a simple way.
  whole:  1.05 (0.33), residues: 716
  helix:  1.26 (0.25), residues: 492
  sheet:  0.28 (0.85), residues: 38
  loop : -0.58 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  96 
 TYR   0.023   0.001   TYR A 698 
 PHE   0.012   0.001   PHE A 575 
 TRP   0.009   0.001   TRP A 736 
 HIS   0.002   0.000   HIS A 461 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5650)
  covalent geometry    : angle       0.59390 ( 7693)
  hydrogen bonds       : bond        0.03008 (  341)
  hydrogen bonds       : angle       4.23395 (  979)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1960.02 seconds
wall clock time: 34 minutes 8.36 seconds (2048.36 seconds total)