Starting phenix.real_space_refine
on Thu Jul 24 09:33:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nvh_12604/07_2025/7nvh_12604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nvh_12604/07_2025/7nvh_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_12604/07_2025/7nvh_12604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2025/7nvh_12604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2025/7nvh_12604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2025/7nvh_12604.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.067
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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.01, per 1000 atoms: 1.27
  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: 1.70
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.55
  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: 1.72

  Time building geometry restraints manager: 1.79 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:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.190
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:18.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.530
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.33), 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
 TRP   0.012   0.001   TRP A 736 
 HIS   0.002   0.001   HIS A 234 
 PHE   0.011   0.001   PHE A 306 
 TYR   0.022   0.001   TYR A 698 
 ARG   0.013   0.001   ARG A  96 

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

*********************** 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  : 0.580 
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: 1.1634
  time to fit residues: 81.3125
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  : 0.617 
-------------------------------------------------------------------------------
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 59 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.109092 restraints weight = 16039.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.54
r_work: 0.3160 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5650  Z= 0.169
  Angle     :  0.666   8.724   7693  Z= 0.330
  Chirality :  0.044   0.235    930
  Planarity :  0.005   0.047    950
  Dihedral  : 16.357 175.940    899
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  5.02 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.33), residues: 716
  helix:  0.44 (0.25), residues: 483
  sheet: -0.56 (0.88), residues: 38
  loop : -0.95 (0.48), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 736 
 HIS   0.002   0.001   HIS A 610 
 PHE   0.009   0.001   PHE A 306 
 TYR   0.025   0.001   TYR A 698 
 ARG   0.003   0.000   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  341)
  hydrogen bonds       : angle       4.71984 (  979)
  covalent geometry    : bond        0.00400 ( 5650)
  covalent geometry    : angle       0.66591 ( 7693)

*********************** 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
  70 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8567 (tp) cc_final: 0.8184 (pp)
REVERT: A  710 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8152 (t70)
  outliers start: 8
  outliers final: 4
  residues processed: 62
  average time/residue: 1.1098
  time to fit residues: 72.4317
Evaluate side-chains
  64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
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 68 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.111996 restraints weight = 16083.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.54
r_work: 0.3178 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1081

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= 0.140
  Angle     :  0.608   8.722   7693  Z= 0.301
  Chirality :  0.042   0.167    930
  Planarity :  0.005   0.046    950
  Dihedral  : 12.822 174.265    899
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  7.27 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.33), residues: 716
  helix:  0.65 (0.25), residues: 489
  sheet: -0.32 (0.86), residues: 38
  loop : -0.99 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 736 
 HIS   0.002   0.001   HIS A 461 
 PHE   0.010   0.001   PHE A 306 
 TYR   0.025   0.001   TYR A 698 
 ARG   0.002   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  341)
  hydrogen bonds       : angle       4.47461 (  979)
  covalent geometry    : bond        0.00325 ( 5650)
  covalent geometry    : angle       0.60810 ( 7693)

*********************** 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
  72 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.580 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8572 (tp) cc_final: 0.8254 (pp)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 1.1574
  time to fit residues: 79.7394
Evaluate side-chains
  63 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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  116 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    0.0570
   chunk 54 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0670
   chunk 19 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.3436

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.113544 restraints weight = 20665.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.01
r_work: 0.3161 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1324

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= 0.109
  Angle     :  0.567   9.993   7693  Z= 0.279
  Chirality :  0.040   0.180    930
  Planarity :  0.005   0.045    950
  Dihedral  : 12.424 177.599    897
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.33), residues: 716
  helix:  0.98 (0.25), residues: 484
  sheet: -0.15 (0.85), residues: 38
  loop : -0.85 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.009   0.001   PHE A 306 
 TYR   0.025   0.001   TYR A 698 
 ARG   0.002   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (  341)
  hydrogen bonds       : angle       4.34147 (  979)
  covalent geometry    : bond        0.00248 ( 5650)
  covalent geometry    : angle       0.56674 ( 7693)

*********************** 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
  78 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6895 (mtp-110)
REVERT: A  406 ILE cc_start: 0.8491 (tp) cc_final: 0.8164 (pp)
  outliers start: 7
  outliers final: 1
  residues processed: 72
  average time/residue: 1.0951
  time to fit residues: 83.2901
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  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3480 r_free = 0.3480 target = 0.124412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.110434 restraints weight = 19617.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.85
r_work: 0.3143 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5650  Z= 0.142
  Angle     :  0.592  10.374   7693  Z= 0.291
  Chirality :  0.041   0.164    930
  Planarity :  0.005   0.045    950
  Dihedral  : 12.480 178.085    897
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.55 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.33), residues: 716
  helix:  1.01 (0.25), residues: 485
  sheet:  0.06 (0.86), residues: 38
  loop : -0.83 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 493 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.024   0.001   PHE A 575 
 TYR   0.021   0.001   TYR A 698 
 ARG   0.008   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  341)
  hydrogen bonds       : angle       4.37036 (  979)
  covalent geometry    : bond        0.00337 ( 5650)
  covalent geometry    : angle       0.59214 ( 7693)

*********************** 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
  71 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8519 (tp) cc_final: 0.8180 (pp)
  outliers start: 7
  outliers final: 2
  residues processed: 64
  average time/residue: 1.0342
  time to fit residues: 70.2899
Evaluate side-chains
  63 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  116 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.124039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.110603 restraints weight = 16827.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.61
r_work: 0.3160 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5650  Z= 0.142
  Angle     :  0.581  10.325   7693  Z= 0.287
  Chirality :  0.041   0.165    930
  Planarity :  0.005   0.044    950
  Dihedral  : 12.550 178.427    897
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.90 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.33), residues: 716
  helix:  1.03 (0.25), residues: 485
  sheet:  0.17 (0.86), residues: 38
  loop : -0.79 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 339 
 PHE   0.020   0.001   PHE A 575 
 TYR   0.026   0.001   TYR A 698 
 ARG   0.006   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  341)
  hydrogen bonds       : angle       4.31751 (  979)
  covalent geometry    : bond        0.00337 ( 5650)
  covalent geometry    : angle       0.58050 ( 7693)

*********************** 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
  71 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.591 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8508 (tp) cc_final: 0.8179 (pp)
REVERT: A  696 MET cc_start: 0.8485 (mmm) cc_final: 0.8279 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 1.1252
  time to fit residues: 77.0353
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  : 0.541 
-------------------------------------------------------------------------------
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 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0670
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0570
   chunk 49 optimal weight:    0.0070
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.3254

-------------------------------------------------------------------------------
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 = 0.3508 r_free = 0.3508 target = 0.126888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.112632 restraints weight = 21401.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.98
r_work: 0.3170 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5650  Z= 0.104
  Angle     :  0.560  11.137   7693  Z= 0.273
  Chirality :  0.040   0.155    930
  Planarity :  0.005   0.044    950
  Dihedral  : 12.494 179.881    897
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.46 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.33), residues: 716
  helix:  1.23 (0.25), residues: 482
  sheet:  0.17 (0.87), residues: 38
  loop : -0.64 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 234 
 PHE   0.019   0.001   PHE A 575 
 TYR   0.024   0.001   TYR A 698 
 ARG   0.006   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03034 (  341)
  hydrogen bonds       : angle       4.25747 (  979)
  covalent geometry    : bond        0.00235 ( 5650)
  covalent geometry    : angle       0.56007 ( 7693)

*********************** 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
  73 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.584 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6880 (mtp-110)
REVERT: A  406 ILE cc_start: 0.8506 (tp) cc_final: 0.8177 (pp)
REVERT: A  696 MET cc_start: 0.8496 (mmm) cc_final: 0.8287 (tpp)
REVERT: A  738 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7384 (tpp-160)
  outliers start: 4
  outliers final: 1
  residues processed: 69
  average time/residue: 1.1201
  time to fit residues: 81.3640
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  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
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 33 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0050
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.125518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111926 restraints weight = 17833.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.70
r_work: 0.3143 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5650  Z= 0.123
  Angle     :  0.580  13.721   7693  Z= 0.280
  Chirality :  0.041   0.160    930
  Planarity :  0.005   0.044    950
  Dihedral  : 12.361 179.454    897
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.80 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.33), residues: 716
  helix:  1.23 (0.25), residues: 484
  sheet:  0.28 (0.87), residues: 38
  loop : -0.56 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.016   0.001   PHE A 575 
 TYR   0.024   0.001   TYR A 698 
 ARG   0.006   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  341)
  hydrogen bonds       : angle       4.25698 (  979)
  covalent geometry    : bond        0.00288 ( 5650)
  covalent geometry    : angle       0.58008 ( 7693)

*********************** 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
  69 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6857 (mtp-110)
REVERT: A  406 ILE cc_start: 0.8477 (tp) cc_final: 0.8145 (pp)
REVERT: A  696 MET cc_start: 0.8517 (mmm) cc_final: 0.8300 (tmm)
REVERT: A  738 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7381 (tpp-160)
  outliers start: 4
  outliers final: 1
  residues processed: 65
  average time/residue: 1.1434
  time to fit residues: 78.5386
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  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ARG
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 27 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.125271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.111530 restraints weight = 18023.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.75
r_work: 0.3166 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1613

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= 0.131
  Angle     :  0.581  12.928   7693  Z= 0.282
  Chirality :  0.041   0.164    930
  Planarity :  0.005   0.044    950
  Dihedral  : 12.177 179.427    897
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.33), residues: 716
  helix:  1.23 (0.25), residues: 484
  sheet:  0.34 (0.88), residues: 38
  loop : -0.56 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.016   0.001   PHE A 575 
 TYR   0.024   0.001   TYR A 698 
 ARG   0.005   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03208 (  341)
  hydrogen bonds       : angle       4.25653 (  979)
  covalent geometry    : bond        0.00309 ( 5650)
  covalent geometry    : angle       0.58124 ( 7693)

*********************** 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
  69 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A  406 ILE cc_start: 0.8487 (tp) cc_final: 0.8148 (pp)
  outliers start: 3
  outliers final: 1
  residues processed: 67
  average time/residue: 1.2035
  time to fit residues: 84.8556
Evaluate side-chains
  64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.125576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112354 restraints weight = 15607.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.52
r_work: 0.3168 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1656

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= 0.125
  Angle     :  0.588  13.700   7693  Z= 0.281
  Chirality :  0.041   0.163    930
  Planarity :  0.005   0.044    950
  Dihedral  : 11.971 179.688    897
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 13.67 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.33), residues: 716
  helix:  1.24 (0.25), residues: 484
  sheet:  0.36 (0.88), residues: 38
  loop : -0.56 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.016   0.001   PHE A 575 
 TYR   0.025   0.001   TYR A 698 
 ARG   0.002   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (  341)
  hydrogen bonds       : angle       4.23528 (  979)
  covalent geometry    : bond        0.00291 ( 5650)
  covalent geometry    : angle       0.58846 ( 7693)

********************** 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
  67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  391 ARG cc_start: 0.7716 (ptp-110) cc_final: 0.6036 (mtt90)
REVERT: A  406 ILE cc_start: 0.8486 (tp) cc_final: 0.8152 (pp)
REVERT: A  696 MET cc_start: 0.8587 (mmm) cc_final: 0.8284 (tpp)
  outliers start: 2
  outliers final: 2
  residues processed: 66
  average time/residue: 1.3386
  time to fit residues: 94.1575
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  : 0.755 
-------------------------------------------------------------------------------
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 55 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.126062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112420 restraints weight = 17125.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.68
r_work: 0.3182 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    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 = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5650  Z= 0.119
  Angle     :  0.577  13.457   7693  Z= 0.278
  Chirality :  0.041   0.162    930
  Planarity :  0.005   0.044    950
  Dihedral  : 11.869 179.966    897
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 13.67 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.33), residues: 716
  helix:  1.28 (0.25), residues: 484
  sheet:  0.36 (0.88), residues: 38
  loop : -0.54 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 736 
 HIS   0.001   0.000   HIS A 610 
 PHE   0.016   0.001   PHE A 575 
 TYR   0.025   0.001   TYR A 698 
 ARG   0.001   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03121 (  341)
  hydrogen bonds       : angle       4.22224 (  979)
  covalent geometry    : bond        0.00276 ( 5650)
  covalent geometry    : angle       0.57683 ( 7693)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3867.42 seconds
wall clock time: 67 minutes 52.57 seconds (4072.57 seconds total)