Starting phenix.real_space_refine
on Mon Jul 28 03:49:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k8a_22724/07_2025/7k8a_22724.cif"
  }
  resolution = 3.65
  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
-------------------------------------------------------------------------------
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=   0.181
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5513 atoms to isotropic.
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      28      5.16       5
     C    3570      2.51       5
     N     913      2.21       5
     O    1002      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5513
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 723, 5513
          Classifications: {'peptide': 723}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 37, 'TRANS': 685}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 4.11, per 1000 atoms: 0.75
  Number of scatterers: 5513
  At special positions: 0
  Unit cell: (92.22, 99.64, 100.7, 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      28     16.00
     O    1002      8.00
     N     913      7.00
     C    3570      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: 1.54
  Conformation dependent library (CDL) restraints added in 926.1 milliseconds
  

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      71.1% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
      removed outlier: 3.661A  pdb=" N   TRP A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE A  12 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 31
      removed outlier: 4.589A  pdb=" N   VAL A  16 " --> pdb=" O   PHE A  12 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 36
      No H-bonds generated for 'chain 'A' and resid 34 through 36'
    Processing helix  chain 'A' and resid 48 through 62
      removed outlier: 3.914A  pdb=" N   ALA A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 4.347A  pdb=" N   SER A  67 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   HIS A  68 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 64 through 68'
    Processing helix  chain 'A' and resid 83 through 101
      removed outlier: 4.169A  pdb=" N   GLN A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 143 through 160
      removed outlier: 3.566A  pdb=" N   ILE A 147 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 170 through 206
      removed outlier: 3.734A  pdb=" N   LEU A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   GLY A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU A 184 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
    Processing helix  chain 'A' and resid 207 through 233
      Proline residue:  A 214  - end of helix
    Processing helix  chain 'A' and resid 241 through 271
      removed outlier: 3.529A  pdb=" N   VAL A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 286
    Processing helix  chain 'A' and resid 286 through 302
      removed outlier: 3.774A  pdb=" N   SER A 301 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 309 through 342
      removed outlier: 4.998A  pdb=" N   ALA A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ALA A 336 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 400
      removed outlier: 4.254A  pdb=" N   ARG A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 415
      Proline residue:  A 407  - end of helix
      removed outlier: 3.678A  pdb=" N   VAL A 410 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 471 through 483
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 525 through 534
      removed outlier: 3.503A  pdb=" N   LYS A 529 " --> pdb=" O   ASP A 525 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASP A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 563
    Processing helix  chain 'A' and resid 563 through 583
      removed outlier: 3.530A  pdb=" N   MET A 567 " --> pdb=" O   LYS A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 612
    Processing helix  chain 'A' and resid 616 through 621
    Processing helix  chain 'A' and resid 630 through 660
      removed outlier: 3.536A  pdb=" N   PHE A 649 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 692
      removed outlier: 4.275A  pdb=" N   ALA A 673 " --> pdb=" O   ARG A 669 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR A 674 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU A 678 " --> pdb=" O   THR A 674 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 681 " --> pdb=" O   ARG A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 722
      removed outlier: 3.791A  pdb=" N   ILE A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 732
    Processing helix  chain 'A' and resid 733 through 737
      removed outlier: 3.624A  pdb=" N   TRP A 737 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 747
      removed outlier: 4.402A  pdb=" N   VAL A 745 " --> pdb=" O   TRP A 741 " (cutoff:3.500A)
    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
      removed outlier: 3.967A  pdb=" N   THR A 133 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518
      removed outlier: 3.523A  pdb=" N   ILE A 516 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A 518 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)

    360 hydrogen bonds defined for protein.
    1053 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: 1.93

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1661
        1.34 -     1.46: 864
        1.46 -     1.58: 3045
        1.58 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 5624
  Sorted by residual:
  bond pdb=" N   ASP A  78 "
       pdb=" CA  ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.458  1.413  0.045 1.33e-02 5.65e+03 1.16e+01
  bond pdb=" CA  THR A  74 "
       pdb=" C   THR A  74 "
    ideal  model  delta    sigma   weight residual
    1.519  1.558 -0.039 1.28e-02 6.10e+03 9.24e+00
  bond pdb=" CA  ASP A  78 "
       pdb=" C   ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.524  1.483  0.041 1.43e-02 4.89e+03 8.40e+00
  bond pdb=" C   THR A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.38e+00
  bond pdb=" C   VAL A 302 "
       pdb=" N   PRO A 303 "
    ideal  model  delta    sigma   weight residual
    1.337  1.361 -0.024 1.11e-02 8.12e+03 4.82e+00
  ... (remaining 5619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 7413
        2.20 -     4.41: 176
        4.41 -     6.61: 50
        6.61 -     8.82: 13
        8.82 -    11.02: 1
  Bond angle restraints: 7653
  Sorted by residual:
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     110.70  117.53   -6.83 1.22e+00 6.72e-01 3.13e+01
  angle pdb=" N   LEU A  73 "
        pdb=" CA  LEU A  73 "
        pdb=" C   LEU A  73 "
      ideal   model   delta    sigma   weight residual
     109.46  116.61   -7.15 1.66e+00 3.63e-01 1.86e+01
  angle pdb=" C   PRO A  75 "
        pdb=" N   PRO A  76 "
        pdb=" CA  PRO A  76 "
      ideal   model   delta    sigma   weight residual
     119.84  114.51    5.33 1.25e+00 6.40e-01 1.82e+01
  angle pdb=" C   ILE A 719 "
        pdb=" N   ARG A 720 "
        pdb=" CA  ARG A 720 "
      ideal   model   delta    sigma   weight residual
     122.38  115.10    7.28 1.81e+00 3.05e-01 1.62e+01
  angle pdb=" N   PHE A 649 "
        pdb=" CA  PHE A 649 "
        pdb=" CB  PHE A 649 "
      ideal   model   delta    sigma   weight residual
     110.28  116.18   -5.90 1.55e+00 4.16e-01 1.45e+01
  ... (remaining 7648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3073
       17.99 -    35.98: 235
       35.98 -    53.97: 45
       53.97 -    71.96: 3
       71.96 -    89.95: 4
  Dihedral angle restraints: 3360
    sinusoidal: 1302
      harmonic: 2058
  Sorted by residual:
  dihedral pdb=" N   PHE A 649 "
           pdb=" C   PHE A 649 "
           pdb=" CA  PHE A 649 "
           pdb=" CB  PHE A 649 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.31  -16.51     0      2.50e+00 1.60e-01 4.36e+01
  dihedral pdb=" C   PHE A 649 "
           pdb=" N   PHE A 649 "
           pdb=" CA  PHE A 649 "
           pdb=" CB  PHE A 649 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.03   16.43     0      2.50e+00 1.60e-01 4.32e+01
  dihedral pdb=" CA  PHE A 722 "
           pdb=" C   PHE A 722 "
           pdb=" N   LEU A 723 "
           pdb=" CA  LEU A 723 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.25  -24.75     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 3357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 905
       0.135 -    0.270: 8
       0.270 -    0.405: 0
       0.405 -    0.540: 0
       0.540 -    0.675: 1
  Chirality restraints: 914
  Sorted by residual:
  chirality pdb=" CA  PHE A 649 "
            pdb=" N   PHE A 649 "
            pdb=" C   PHE A 649 "
            pdb=" CB  PHE A 649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CB  ILE A 137 "
            pdb=" CA  ILE A 137 "
            pdb=" CG1 ILE A 137 "
            pdb=" CG2 ILE A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.77e-01
  chirality pdb=" CA  ILE A 135 "
            pdb=" N   ILE A 135 "
            pdb=" C   ILE A 135 "
            pdb=" CB  ILE A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 911 not shown)

  Planarity restraints: 967
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 406 "   -0.050 5.00e-02 4.00e+02   7.47e-02 8.92e+00
        pdb=" N   PRO A 407 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 417 "    0.029 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A 418 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 649 "    0.016 2.00e-02 2.50e+03   1.29e-02 2.91e+00
        pdb=" CG  PHE A 649 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 649 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 649 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 649 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 649 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 649 "    0.001 2.00e-02 2.50e+03
  ... (remaining 964 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 936
        2.76 -     3.30: 5906
        3.30 -     3.83: 9048
        3.83 -     4.37: 10106
        4.37 -     4.90: 16840
  Nonbonded interactions: 42836
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 142 "
            pdb=" OE2 GLU A 146 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" O   MET A 610 "
            pdb=" OH  TYR A 622 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" O   VAL A 513 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR A 680 "
            pdb=" NH2 ARG A 720 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   GLY A 426 "
            pdb=" OH  TYR A 431 "
     model   vdw
     2.306 3.040
  ... (remaining 42831 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.750
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5519
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      :  0.004   0.045   5624  Z= 0.226
  Angle     :  0.918  11.022   7653  Z= 0.501
  Chirality :  0.052   0.675    914
  Planarity :  0.006   0.075    967
  Dihedral  : 13.382  89.947   2036
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.19 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.15 %
  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: -1.30 (0.30), residues: 719
  helix: -0.15 (0.24), residues: 457
  sheet: -3.15 (0.69), residues: 31
  loop : -1.78 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 737 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.029   0.002   PHE A 649 
 TYR   0.025   0.002   TYR A 151 
 ARG   0.006   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13154 (  360)
  hydrogen bonds       : angle       5.64963 ( 1053)
  covalent geometry    : bond        0.00402 ( 5624)
  covalent geometry    : angle       0.91844 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7275 (tp-100)
REVERT: A  147 ILE cc_start: 0.8233 (pt) cc_final: 0.7427 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.1547
  time to fit residues: 27.0217
Evaluate side-chains
  117 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.263961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.245821 restraints weight = 9221.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.250798 restraints weight = 7636.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.253251 restraints weight = 4003.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.4597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5705
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5624  Z= 0.194
  Angle     :  0.818   8.159   7653  Z= 0.414
  Chirality :  0.046   0.185    914
  Planarity :  0.006   0.068    967
  Dihedral  :  5.485  24.545    769
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.87 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 11.73 %
    Favored  : 84.86 %
  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: -1.31 (0.30), residues: 719
  helix: -0.07 (0.23), residues: 458
  sheet: -3.30 (0.68), residues: 30
  loop : -2.00 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 737 
 HIS   0.006   0.002   HIS A 540 
 PHE   0.018   0.002   PHE A 649 
 TYR   0.016   0.002   TYR A 151 
 ARG   0.006   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05099 (  360)
  hydrogen bonds       : angle       5.11878 ( 1053)
  covalent geometry    : bond        0.00409 ( 5624)
  covalent geometry    : angle       0.81825 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7216 (m-10) cc_final: 0.6783 (m-10)
REVERT: A  128 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7139 (tp-100)
REVERT: A  419 LEU cc_start: 0.6405 (pp) cc_final: 0.6200 (pp)
  outliers start: 20
  outliers final: 15
  residues processed: 127
  average time/residue: 0.2048
  time to fit residues: 35.2669
Evaluate side-chains
  129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.265560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.248823 restraints weight = 9244.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.251285 restraints weight = 6717.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.253283 restraints weight = 4601.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5661
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5624  Z= 0.148
  Angle     :  0.747   8.271   7653  Z= 0.370
  Chirality :  0.044   0.290    914
  Planarity :  0.006   0.056    967
  Dihedral  :  5.215  21.656    767
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.73 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 14.46 %
    Favored  : 81.97 %
  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 (0.31), residues: 719
  helix:  0.17 (0.24), residues: 460
  sheet: -3.21 (0.68), residues: 42
  loop : -1.91 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 737 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.021   0.002   PHE A 449 
 TYR   0.019   0.002   TYR A 151 
 ARG   0.008   0.001   ARG A 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04462 (  360)
  hydrogen bonds       : angle       4.83899 ( 1053)
  covalent geometry    : bond        0.00314 ( 5624)
  covalent geometry    : angle       0.74655 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7200 (m-10) cc_final: 0.6741 (m-10)
REVERT: A  128 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7039 (tp-100)
REVERT: A  693 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.6232 (m-10)
REVERT: A  742 MET cc_start: -0.2221 (tpt) cc_final: -0.3336 (tpt)
  outliers start: 21
  outliers final: 17
  residues processed: 129
  average time/residue: 0.2488
  time to fit residues: 42.5050
Evaluate side-chains
  132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  693 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.0170
   chunk 55 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0870
   chunk 32 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0770
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.3354

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.271733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.254084 restraints weight = 9436.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.257736 restraints weight = 5999.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.260277 restraints weight = 4091.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5507
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5624  Z= 0.132
  Angle     :  0.708   7.864   7653  Z= 0.345
  Chirality :  0.043   0.208    914
  Planarity :  0.005   0.047    967
  Dihedral  :  4.830  20.021    767
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.67 %
    Favored  : 79.25 %
  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: -0.61 (0.31), residues: 719
  helix:  0.56 (0.24), residues: 466
  sheet: -2.96 (0.73), residues: 36
  loop : -2.00 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 111 
 HIS   0.002   0.000   HIS A  68 
 PHE   0.017   0.001   PHE A 265 
 TYR   0.017   0.001   TYR A 151 
 ARG   0.007   0.000   ARG A 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  360)
  hydrogen bonds       : angle       4.60338 ( 1053)
  covalent geometry    : bond        0.00278 ( 5624)
  covalent geometry    : angle       0.70762 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A  248 LEU cc_start: 0.7328 (mm) cc_final: 0.6933 (mm)
REVERT: A  253 ILE cc_start: 0.7039 (mm) cc_final: 0.6738 (mm)
REVERT: A  273 TYR cc_start: 0.5964 (m-10) cc_final: 0.4772 (m-10)
REVERT: A  631 MET cc_start: 0.6673 (tpt) cc_final: 0.6472 (mmm)
REVERT: A  742 MET cc_start: -0.1932 (tpt) cc_final: -0.3281 (tpt)
  outliers start: 24
  outliers final: 17
  residues processed: 126
  average time/residue: 0.1692
  time to fit residues: 27.9630
Evaluate side-chains
  131 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  721 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.260117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.241905 restraints weight = 9198.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.247256 restraints weight = 8267.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.249509 restraints weight = 4172.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5779
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5624  Z= 0.224
  Angle     :  0.823   7.701   7653  Z= 0.418
  Chirality :  0.047   0.390    914
  Planarity :  0.006   0.043    967
  Dihedral  :  5.359  22.307    767
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.98 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 18.54 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.31), residues: 719
  helix:  0.17 (0.24), residues: 467
  sheet: -3.52 (0.68), residues: 34
  loop : -1.98 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  86 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.025   0.003   PHE A 649 
 TYR   0.014   0.002   TYR A 151 
 ARG   0.013   0.001   ARG A 720 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04952 (  360)
  hydrogen bonds       : angle       5.01963 ( 1053)
  covalent geometry    : bond        0.00485 ( 5624)
  covalent geometry    : angle       0.82336 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.7490 (tp40) cc_final: 0.7273 (tp-100)
REVERT: A  271 GLU cc_start: 0.5230 (mt-10) cc_final: 0.4638 (mt-10)
REVERT: A  273 TYR cc_start: 0.6503 (m-10) cc_final: 0.5332 (m-10)
REVERT: A  480 LYS cc_start: 0.6436 (mmtm) cc_final: 0.5366 (mttm)
REVERT: A  631 MET cc_start: 0.7027 (tpt) cc_final: 0.6565 (mmm)
REVERT: A  742 MET cc_start: -0.1994 (tpt) cc_final: -0.3278 (tpt)
  outliers start: 30
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1765
  time to fit residues: 30.0155
Evaluate side-chains
  135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0050
   chunk 24 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    2.5398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.265526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.247792 restraints weight = 9178.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.253419 restraints weight = 7955.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.255801 restraints weight = 3762.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.4615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5688
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5624  Z= 0.153
  Angle     :  0.750   7.588   7653  Z= 0.371
  Chirality :  0.044   0.255    914
  Planarity :  0.005   0.042    967
  Dihedral  :  5.181  22.258    767
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.73 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 20.41 %
    Favored  : 74.32 %
  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: -0.86 (0.31), residues: 719
  helix:  0.35 (0.24), residues: 462
  sheet: -3.44 (0.67), residues: 42
  loop : -1.85 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.019   0.002   PHE A 649 
 TYR   0.019   0.002   TYR A 151 
 ARG   0.008   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04400 (  360)
  hydrogen bonds       : angle       4.85282 ( 1053)
  covalent geometry    : bond        0.00337 ( 5624)
  covalent geometry    : angle       0.75000 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A  125 MET cc_start: 0.6443 (ttt) cc_final: 0.6161 (ttt)
REVERT: A  480 LYS cc_start: 0.6203 (mmtm) cc_final: 0.5243 (mttm)
REVERT: A  534 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6901 (mmt-90)
REVERT: A  631 MET cc_start: 0.6950 (tpt) cc_final: 0.6592 (mmm)
REVERT: A  742 MET cc_start: -0.1879 (tpt) cc_final: -0.3142 (tpt)
  outliers start: 31
  outliers final: 24
  residues processed: 132
  average time/residue: 0.3593
  time to fit residues: 62.1406
Evaluate side-chains
  132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.262813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.245186 restraints weight = 9314.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.250191 restraints weight = 8154.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.252059 restraints weight = 4561.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.4596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5731
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5624  Z= 0.164
  Angle     :  0.776  10.049   7653  Z= 0.382
  Chirality :  0.045   0.352    914
  Planarity :  0.006   0.042    967
  Dihedral  :  5.228  22.692    767
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.56 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.43 %
    Favored  : 73.64 %
  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: -0.84 (0.31), residues: 719
  helix:  0.37 (0.24), residues: 461
  sheet: -3.63 (0.65), residues: 42
  loop : -1.78 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.019   0.002   PHE A 649 
 TYR   0.020   0.002   TYR A 151 
 ARG   0.006   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  360)
  hydrogen bonds       : angle       4.90358 ( 1053)
  covalent geometry    : bond        0.00358 ( 5624)
  covalent geometry    : angle       0.77556 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7168 (m-10) cc_final: 0.6742 (m-10)
REVERT: A  480 LYS cc_start: 0.6353 (mmtm) cc_final: 0.5371 (mttm)
REVERT: A  534 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.6911 (mmt-90)
REVERT: A  631 MET cc_start: 0.7026 (tpt) cc_final: 0.6604 (mmm)
REVERT: A  662 MET cc_start: 0.5228 (mmm) cc_final: 0.4924 (mmm)
REVERT: A  742 MET cc_start: -0.2186 (tpt) cc_final: -0.3399 (tpt)
  outliers start: 29
  outliers final: 26
  residues processed: 125
  average time/residue: 0.1697
  time to fit residues: 27.7118
Evaluate side-chains
  134 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 52 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.258480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.241404 restraints weight = 9172.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.246689 restraints weight = 8434.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.248891 restraints weight = 4091.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5817
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5624  Z= 0.213
  Angle     :  0.841   8.563   7653  Z= 0.423
  Chirality :  0.046   0.283    914
  Planarity :  0.006   0.048    967
  Dihedral  :  5.624  25.305    767
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.95 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 21.94 %
    Favored  : 72.79 %
  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: -1.21 (0.31), residues: 719
  helix:  0.09 (0.24), residues: 464
  sheet: -3.75 (0.65), residues: 34
  loop : -2.11 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 737 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.026   0.002   PHE A 389 
 TYR   0.023   0.003   TYR A 151 
 ARG   0.017   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05057 (  360)
  hydrogen bonds       : angle       5.20731 ( 1053)
  covalent geometry    : bond        0.00462 ( 5624)
  covalent geometry    : angle       0.84114 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7323 (m-10) cc_final: 0.6713 (m-10)
REVERT: A  480 LYS cc_start: 0.6355 (mmtm) cc_final: 0.5386 (mmtm)
REVERT: A  664 THR cc_start: 0.3561 (OUTLIER) cc_final: 0.2421 (m)
REVERT: A  742 MET cc_start: -0.1958 (tpt) cc_final: -0.3235 (tpt)
  outliers start: 31
  outliers final: 24
  residues processed: 129
  average time/residue: 0.1592
  time to fit residues: 27.0122
Evaluate side-chains
  137 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   68 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   overall best weight:    3.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.261361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.244809 restraints weight = 9290.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.250275 restraints weight = 8344.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.252053 restraints weight = 3799.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5747
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5624  Z= 0.171
  Angle     :  0.818   9.105   7653  Z= 0.402
  Chirality :  0.045   0.253    914
  Planarity :  0.006   0.072    967
  Dihedral  :  5.411  21.706    767
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.42 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 22.45 %
    Favored  : 72.11 %
  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: -0.99 (0.31), residues: 719
  helix:  0.26 (0.24), residues: 459
  sheet: -3.75 (0.66), residues: 34
  loop : -1.95 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  86 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.021   0.002   PHE A 265 
 TYR   0.023   0.002   TYR A 151 
 ARG   0.014   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  360)
  hydrogen bonds       : angle       5.06975 ( 1053)
  covalent geometry    : bond        0.00378 ( 5624)
  covalent geometry    : angle       0.81811 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7311 (m-10) cc_final: 0.6696 (m-10)
REVERT: A  104 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7142 (mm-40)
REVERT: A  470 THR cc_start: 0.5754 (OUTLIER) cc_final: 0.5063 (p)
REVERT: A  480 LYS cc_start: 0.6160 (mmtm) cc_final: 0.5154 (mttm)
REVERT: A  579 MET cc_start: 0.5978 (mmm) cc_final: 0.5673 (mmm)
REVERT: A  642 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7310 (tt)
REVERT: A  662 MET cc_start: 0.5295 (mmm) cc_final: 0.4896 (mmm)
REVERT: A  664 THR cc_start: 0.3320 (OUTLIER) cc_final: 0.2133 (m)
REVERT: A  742 MET cc_start: -0.2053 (tpt) cc_final: -0.3304 (tpt)
  outliers start: 32
  outliers final: 28
  residues processed: 136
  average time/residue: 0.1680
  time to fit residues: 30.0179
Evaluate side-chains
  144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0060
   chunk 23 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    2.5802

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.262801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.245173 restraints weight = 9301.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.250534 restraints weight = 8492.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.252405 restraints weight = 4128.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.4595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5736
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5624  Z= 0.162
  Angle     :  0.808   9.144   7653  Z= 0.397
  Chirality :  0.046   0.356    914
  Planarity :  0.006   0.071    967
  Dihedral  :  5.360  21.493    767
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.42 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 22.45 %
    Favored  : 72.11 %
  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: -0.99 (0.31), residues: 719
  helix:  0.32 (0.24), residues: 461
  sheet: -3.74 (0.65), residues: 42
  loop : -1.99 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.020   0.002   PHE A 265 
 TYR   0.046   0.003   TYR A 273 
 ARG   0.015   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04509 (  360)
  hydrogen bonds       : angle       5.01561 ( 1053)
  covalent geometry    : bond        0.00360 ( 5624)
  covalent geometry    : angle       0.80803 ( 7653)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A   44 TYR cc_start: 0.7278 (m-10) cc_final: 0.6767 (m-10)
REVERT: A  470 THR cc_start: 0.5757 (OUTLIER) cc_final: 0.5069 (p)
REVERT: A  480 LYS cc_start: 0.5986 (mmtm) cc_final: 0.4980 (mttm)
REVERT: A  579 MET cc_start: 0.5910 (mmm) cc_final: 0.5590 (mmm)
REVERT: A  642 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7351 (tt)
REVERT: A  662 MET cc_start: 0.5280 (mmm) cc_final: 0.4918 (mmm)
REVERT: A  664 THR cc_start: 0.3526 (OUTLIER) cc_final: 0.2296 (m)
REVERT: A  742 MET cc_start: -0.2184 (tpt) cc_final: -0.3376 (tpt)
  outliers start: 32
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1587
  time to fit residues: 27.8508
Evaluate side-chains
  144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   68 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  721 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0980
   chunk 44 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    4.6188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.259032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.240932 restraints weight = 9363.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.246429 restraints weight = 8460.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.248582 restraints weight = 4059.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5811
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5624  Z= 0.206
  Angle     :  0.861   8.964   7653  Z= 0.431
  Chirality :  0.047   0.402    914
  Planarity :  0.007   0.066    967
  Dihedral  :  5.637  28.705    767
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.82 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 22.79 %
    Favored  : 72.11 %
  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: -1.15 (0.31), residues: 719
  helix:  0.15 (0.24), residues: 460
  sheet: -3.73 (0.68), residues: 34
  loop : -2.07 (0.39), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 108 
 HIS   0.006   0.002   HIS A 540 
 PHE   0.024   0.002   PHE A 389 
 TYR   0.037   0.003   TYR A 273 
 ARG   0.018   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04871 (  360)
  hydrogen bonds       : angle       5.22157 ( 1053)
  covalent geometry    : bond        0.00451 ( 5624)
  covalent geometry    : angle       0.86123 ( 7653)

===============================================================================
Job complete
usr+sys time: 2281.85 seconds
wall clock time: 43 minutes 7.47 seconds (2587.47 seconds total)