Starting phenix.real_space_refine
on Wed Jun  4 16:14:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hrm_34978/06_2025/8hrm_34978.cif"
  }
  resolution = 2.56
  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=   0.009 sd=   0.064
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: 3
    Type Number    sf(0)   Gaussians
     C    2224      2.51       5
     N     620      2.21       5
     O     723      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3567
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 887
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 887
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 887
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 887
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.74, per 1000 atoms: 0.77
  Number of scatterers: 3567
  At special positions: 0
  Unit cell: (68.0021, 57.6201, 62.8111, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     723      8.00
     N     620      7.00
     C    2224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 425.7 milliseconds
  

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  824

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 4 sheets defined
      4.2% alpha, 49.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 122
      removed outlier: 3.589A  pdb=" N   SER A 122 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 122
      removed outlier: 3.553A  pdb=" N   SER B 122 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 122
      removed outlier: 3.585A  pdb=" N   SER C 122 " --> pdb=" O   ALA C 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 122
      removed outlier: 3.601A  pdb=" N   SER D 122 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23
      removed outlier: 5.401A  pdb=" N   VAL A  55 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ALA A  78 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   SER A  88 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 23
      removed outlier: 5.385A  pdb=" N   VAL B  55 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA B  78 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   SER B  88 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 23
      removed outlier: 5.432A  pdb=" N   VAL C  55 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA C  78 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER C  88 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 23
      removed outlier: 5.385A  pdb=" N   VAL D  55 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   ALA D  78 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER D  88 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 572
        1.29 -     1.35: 584
        1.35 -     1.42: 480
        1.42 -     1.48: 620
        1.48 -     1.55: 1380
  Bond restraints: 3636
  Sorted by residual:
  bond pdb=" CB  THR D  91 "
       pdb=" CG2 THR D  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.23e+00
  bond pdb=" CG  LEU B 109 "
       pdb=" CD1 LEU B 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.68e+00
  bond pdb=" CG  LEU A 109 "
       pdb=" CD1 LEU A 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.53e+00
  bond pdb=" CB  THR B  91 "
       pdb=" CG2 THR B  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.42e+00
  bond pdb=" CG  LEU C 109 "
       pdb=" CD1 LEU C 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.31e+00
  ... (remaining 3631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 4820
        1.81 -     3.63: 113
        3.63 -     5.44: 25
        5.44 -     7.25: 12
        7.25 -     9.07: 6
  Bond angle restraints: 4976
  Sorted by residual:
  angle pdb=" N   GLU B  44 "
        pdb=" CA  GLU B  44 "
        pdb=" C   GLU B  44 "
      ideal   model   delta    sigma   weight residual
     108.07  113.07   -5.00 1.38e+00 5.25e-01 1.31e+01
  angle pdb=" N   GLU A  44 "
        pdb=" CA  GLU A  44 "
        pdb=" C   GLU A  44 "
      ideal   model   delta    sigma   weight residual
     108.07  112.96   -4.89 1.38e+00 5.25e-01 1.26e+01
  angle pdb=" N   GLU C  44 "
        pdb=" CA  GLU C  44 "
        pdb=" C   GLU C  44 "
      ideal   model   delta    sigma   weight residual
     108.07  112.87   -4.80 1.38e+00 5.25e-01 1.21e+01
  angle pdb=" N   GLU D  44 "
        pdb=" CA  GLU D  44 "
        pdb=" C   GLU D  44 "
      ideal   model   delta    sigma   weight residual
     108.07  112.77   -4.70 1.38e+00 5.25e-01 1.16e+01
  angle pdb=" C   GLU C  44 "
        pdb=" CA  GLU C  44 "
        pdb=" CB  GLU C  44 "
      ideal   model   delta    sigma   weight residual
     114.41  106.87    7.54 2.30e+00 1.89e-01 1.08e+01
  ... (remaining 4971 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.61: 1689
       14.61 -    29.23: 208
       29.23 -    43.84: 58
       43.84 -    58.45: 25
       58.45 -    73.06: 4
  Dihedral angle restraints: 1984
    sinusoidal: 664
      harmonic: 1320
  Sorted by residual:
  dihedral pdb=" CA  TRP D  79 "
           pdb=" C   TRP D  79 "
           pdb=" N   LYS D  80 "
           pdb=" CA  LYS D  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.60   23.40     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  TRP B  79 "
           pdb=" C   TRP B  79 "
           pdb=" N   LYS B  80 "
           pdb=" CA  LYS B  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.44   22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  GLU C  44 "
           pdb=" C   GLU C  44 "
           pdb=" N   SER C  45 "
           pdb=" CA  SER C  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 1981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 297
       0.032 -    0.064: 193
       0.064 -    0.096: 32
       0.096 -    0.129: 20
       0.129 -    0.161: 14
  Chirality restraints: 556
  Sorted by residual:
  chirality pdb=" CA  SER C  45 "
            pdb=" N   SER C  45 "
            pdb=" C   SER C  45 "
            pdb=" CB  SER C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  TRP D  79 "
            pdb=" N   TRP D  79 "
            pdb=" C   TRP D  79 "
            pdb=" CB  TRP D  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" CA  TRP B  79 "
            pdb=" N   TRP B  79 "
            pdb=" C   TRP B  79 "
            pdb=" CB  TRP B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 553 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  79 "    0.021 2.00e-02 2.50e+03   1.35e-02 4.53e+00
        pdb=" CG  TRP D  79 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  79 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  79 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  79 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  79 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  79 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  79 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  79 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  79 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  79 "    0.020 2.00e-02 2.50e+03   1.23e-02 3.76e+00
        pdb=" CG  TRP B  79 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  79 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  79 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  79 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  79 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  79 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  79 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  79 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  79 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  79 "   -0.019 2.00e-02 2.50e+03   1.17e-02 3.44e+00
        pdb=" CG  TRP A  79 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  79 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  79 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  79 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  79 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  79 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  79 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  79 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 161
        2.69 -     3.24: 3401
        3.24 -     3.80: 6327
        3.80 -     4.35: 8100
        4.35 -     4.90: 13882
  Nonbonded interactions: 31871
  Sorted by model distance:
  nonbonded pdb=" O   THR D  57 "
            pdb=" O   HOH D 201 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG  SER B  93 "
            pdb=" OG1 THR D 111 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG1 THR B 111 "
            pdb=" OG  SER D  93 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OG  SER A  93 "
            pdb=" OG1 THR C 111 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG1 THR A 111 "
            pdb=" OG  SER C  93 "
     model   vdw
     2.201 3.040
  ... (remaining 31866 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.100
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3636  Z= 0.234
  Angle     :  0.817   9.066   4976  Z= 0.424
  Chirality :  0.047   0.161    556
  Planarity :  0.004   0.053    624
  Dihedral  : 15.716  73.064   1160
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  5.98 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.78 %
    Favored  : 67.15 %
  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: -1.82 (0.38), residues: 468
  helix: -3.02 (0.74), residues: 24
  sheet: -1.36 (0.28), residues: 284
  loop : -0.11 (0.54), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP D  79 
 HIS   0.004   0.002   HIS A  87 
 PHE   0.011   0.002   PHE C  29 
 TYR   0.022   0.002   TYR B  54 
 ARG   0.010   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24011 (  184)
  hydrogen bonds       : angle      11.60207 (  480)
  covalent geometry    : bond        0.00518 ( 3636)
  covalent geometry    : angle       0.81667 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.359 
Fit side-chains
  outliers start: 14
  outliers final: 9
  residues processed: 81
  average time/residue: 0.6195
  time to fit residues: 53.1384
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 33 optimal weight:   10.0000
   chunk 18 optimal weight:    0.1980
   chunk 11 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 ASN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.196274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.172110 restraints weight = 4486.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 2.42
r_work: 0.4097 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3636  Z= 0.134
  Angle     :  0.667   5.779   4976  Z= 0.353
  Chirality :  0.045   0.145    556
  Planarity :  0.004   0.037    624
  Dihedral  :  5.982  24.064    521
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  5.77 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 22.97 %
    Favored  : 69.48 %
  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: -1.58 (0.38), residues: 468
  helix: -2.89 (0.72), residues: 24
  sheet: -1.15 (0.27), residues: 288
  loop : -0.02 (0.55), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  79 
 HIS   0.002   0.001   HIS D 127 
 PHE   0.007   0.001   PHE C  29 
 TYR   0.009   0.001   TYR C  54 
 ARG   0.006   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  184)
  hydrogen bonds       : angle       8.11319 (  480)
  covalent geometry    : bond        0.00290 ( 3636)
  covalent geometry    : angle       0.66700 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A   95 GLN cc_start: 0.8052 (pt0) cc_final: 0.7816 (pt0)
  outliers start: 26
  outliers final: 14
  residues processed: 86
  average time/residue: 0.6483
  time to fit residues: 58.7287
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   39 LEU
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 ASN
** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.192019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.164113 restraints weight = 4450.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 2.52
r_work: 0.4003 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   3636  Z= 0.288
  Angle     :  0.797   6.358   4976  Z= 0.414
  Chirality :  0.049   0.159    556
  Planarity :  0.004   0.049    624
  Dihedral  :  6.659  28.811    519
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  5.34 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 27.33 %
    Favored  : 64.53 %
  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: -1.58 (0.38), residues: 468
  helix: -2.85 (0.79), residues: 24
  sheet: -1.06 (0.28), residues: 280
  loop : -0.29 (0.53), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.005   0.002   HIS A  87 
 PHE   0.014   0.003   PHE B  29 
 TYR   0.015   0.002   TYR B  54 
 ARG   0.012   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  184)
  hydrogen bonds       : angle       7.99783 (  480)
  covalent geometry    : bond        0.00659 ( 3636)
  covalent geometry    : angle       0.79712 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.371 
Fit side-chains
REVERT: B   79 TRP cc_start: 0.7067 (m100) cc_final: 0.6646 (m-90)
  outliers start: 28
  outliers final: 15
  residues processed: 86
  average time/residue: 0.8055
  time to fit residues: 72.4607
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0670
   chunk 22 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0470
   chunk 3 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4430 r_free = 0.4430 target = 0.196295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.170203 restraints weight = 4489.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.54
r_work: 0.4057 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3636  Z= 0.133
  Angle     :  0.656   5.959   4976  Z= 0.339
  Chirality :  0.044   0.145    556
  Planarity :  0.004   0.054    624
  Dihedral  :  5.935  26.900    519
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 28.49 %
    Favored  : 63.95 %
  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: -1.46 (0.37), residues: 468
  helix: -2.57 (0.82), residues: 24
  sheet: -0.87 (0.28), residues: 280
  loop : -0.51 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  92 
 HIS   0.001   0.001   HIS A  87 
 PHE   0.009   0.002   PHE C  29 
 TYR   0.008   0.001   TYR C  54 
 ARG   0.014   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03011 (  184)
  hydrogen bonds       : angle       7.42507 (  480)
  covalent geometry    : bond        0.00295 ( 3636)
  covalent geometry    : angle       0.65565 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   95 GLN cc_start: 0.8085 (pt0) cc_final: 0.7863 (pt0)
REVERT: B   53 ARG cc_start: 0.6710 (tpp80) cc_final: 0.6354 (tpp-160)
REVERT: B   79 TRP cc_start: 0.7133 (m100) cc_final: 0.6663 (m-90)
REVERT: D   79 TRP cc_start: 0.7099 (m100) cc_final: 0.6385 (m-90)
  outliers start: 26
  outliers final: 17
  residues processed: 81
  average time/residue: 0.6922
  time to fit residues: 59.2285
Evaluate side-chains
  78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   39 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4383 r_free = 0.4383 target = 0.192069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.164848 restraints weight = 4541.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 2.52
r_work: 0.4006 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   3636  Z= 0.249
  Angle     :  0.768   8.847   4976  Z= 0.395
  Chirality :  0.047   0.153    556
  Planarity :  0.003   0.034    624
  Dihedral  :  6.620  45.222    519
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 30.52 %
    Favored  : 61.92 %
  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: -1.62 (0.37), residues: 468
  helix: -2.82 (0.75), residues: 24
  sheet: -1.01 (0.28), residues: 280
  loop : -0.51 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  75 
 HIS   0.004   0.002   HIS A  87 
 PHE   0.013   0.002   PHE A  29 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.007   0.001   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  184)
  hydrogen bonds       : angle       7.54510 (  480)
  covalent geometry    : bond        0.00567 ( 3636)
  covalent geometry    : angle       0.76826 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 62
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B   79 TRP cc_start: 0.7065 (m100) cc_final: 0.6342 (m-90)
REVERT: D   79 TRP cc_start: 0.6982 (m100) cc_final: 0.6454 (m-90)
  outliers start: 26
  outliers final: 16
  residues processed: 80
  average time/residue: 0.7797
  time to fit residues: 65.2630
Evaluate side-chains
  77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4409 r_free = 0.4409 target = 0.194598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.169099 restraints weight = 4538.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 2.47
r_work: 0.4051 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3636  Z= 0.147
  Angle     :  0.684   6.560   4976  Z= 0.349
  Chirality :  0.044   0.142    556
  Planarity :  0.003   0.037    624
  Dihedral  :  6.342  54.286    519
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 33.72 %
    Favored  : 59.88 %
  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: -1.59 (0.36), residues: 468
  helix: -2.46 (0.82), residues: 24
  sheet: -1.00 (0.28), residues: 280
  loop : -0.52 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  75 
 HIS   0.002   0.000   HIS A  87 
 PHE   0.010   0.002   PHE B  29 
 TYR   0.009   0.001   TYR C  54 
 ARG   0.009   0.001   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02947 (  184)
  hydrogen bonds       : angle       7.15962 (  480)
  covalent geometry    : bond        0.00332 ( 3636)
  covalent geometry    : angle       0.68407 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7058 (m100) cc_final: 0.6283 (m-90)
REVERT: A   84 ARG cc_start: 0.7318 (mtp180) cc_final: 0.7114 (mtp180)
REVERT: B   53 ARG cc_start: 0.6686 (tpp80) cc_final: 0.6398 (tpp-160)
REVERT: B   79 TRP cc_start: 0.7135 (m100) cc_final: 0.6302 (m-90)
REVERT: D   79 TRP cc_start: 0.7070 (m100) cc_final: 0.6388 (m-90)
REVERT: D   84 ARG cc_start: 0.7184 (ttm110) cc_final: 0.6955 (ptm160)
  outliers start: 22
  outliers final: 15
  residues processed: 73
  average time/residue: 0.7535
  time to fit residues: 57.6990
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4382 r_free = 0.4382 target = 0.192048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.164650 restraints weight = 4462.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 2.47
r_work: 0.4002 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   3636  Z= 0.261
  Angle     :  0.796   6.532   4976  Z= 0.411
  Chirality :  0.048   0.157    556
  Planarity :  0.004   0.041    624
  Dihedral  :  6.744  47.405    519
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 31.10 %
    Favored  : 62.21 %
  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: -1.78 (0.36), residues: 468
  helix: -2.64 (0.78), residues: 24
  sheet: -1.16 (0.28), residues: 280
  loop : -0.57 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  75 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.013   0.002   PHE B  29 
 TYR   0.012   0.002   TYR C  54 
 ARG   0.009   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  184)
  hydrogen bonds       : angle       7.46982 (  480)
  covalent geometry    : bond        0.00597 ( 3636)
  covalent geometry    : angle       0.79559 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7081 (m100) cc_final: 0.6433 (m-90)
REVERT: B  107 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7591 (mt0)
REVERT: D   79 TRP cc_start: 0.6971 (m100) cc_final: 0.6400 (m-90)
REVERT: D   84 ARG cc_start: 0.7287 (ttm110) cc_final: 0.6979 (ptm160)
  outliers start: 23
  outliers final: 16
  residues processed: 81
  average time/residue: 0.8744
  time to fit residues: 74.0951
Evaluate side-chains
  81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  107 GLN
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4385 r_free = 0.4385 target = 0.192298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.165538 restraints weight = 4486.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 2.52
r_work: 0.4024 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3636  Z= 0.203
  Angle     :  0.776   7.127   4976  Z= 0.399
  Chirality :  0.048   0.171    556
  Planarity :  0.004   0.047    624
  Dihedral  :  6.711  52.722    519
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 31.98 %
    Favored  : 61.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -1.85 (0.36), residues: 468
  helix: -2.74 (0.75), residues: 24
  sheet: -1.21 (0.27), residues: 280
  loop : -0.59 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.002   0.001   HIS A 127 
 PHE   0.012   0.002   PHE A  29 
 TYR   0.011   0.001   TYR C  54 
 ARG   0.012   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (  184)
  hydrogen bonds       : angle       7.31550 (  480)
  covalent geometry    : bond        0.00463 ( 3636)
  covalent geometry    : angle       0.77556 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7107 (m100) cc_final: 0.6332 (m-90)
REVERT: B   79 TRP cc_start: 0.7055 (m100) cc_final: 0.6245 (m-90)
REVERT: B   84 ARG cc_start: 0.7331 (ttm110) cc_final: 0.7044 (ptm160)
REVERT: C   53 ARG cc_start: 0.6618 (tpp80) cc_final: 0.6281 (tpp-160)
REVERT: D   79 TRP cc_start: 0.7025 (m100) cc_final: 0.6343 (m-90)
REVERT: D   84 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6922 (ptm160)
  outliers start: 23
  outliers final: 15
  residues processed: 82
  average time/residue: 0.7358
  time to fit residues: 63.3768
Evaluate side-chains
  81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0770
   chunk 43 optimal weight:    0.2980
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.8744

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4379 r_free = 0.4379 target = 0.191345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.165142 restraints weight = 4413.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.4115 rms_B_bonded: 2.46
r_work: 0.4021 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3636  Z= 0.229
  Angle     :  0.824   7.169   4976  Z= 0.423
  Chirality :  0.049   0.170    556
  Planarity :  0.004   0.041    624
  Dihedral  :  6.746  51.362    519
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 34.01 %
    Favored  : 60.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.35), residues: 468
  helix: -2.80 (0.74), residues: 24
  sheet: -1.26 (0.28), residues: 280
  loop : -0.67 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  75 
 HIS   0.002   0.001   HIS D 127 
 PHE   0.014   0.002   PHE B  29 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.009   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  184)
  hydrogen bonds       : angle       7.36568 (  480)
  covalent geometry    : bond        0.00524 ( 3636)
  covalent geometry    : angle       0.82419 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7103 (m100) cc_final: 0.6332 (m-90)
REVERT: A  101 GLU cc_start: 0.6732 (pp20) cc_final: 0.6259 (pp20)
REVERT: B   84 ARG cc_start: 0.7338 (ttm110) cc_final: 0.7034 (ptm160)
REVERT: D   79 TRP cc_start: 0.7024 (m100) cc_final: 0.6423 (m-90)
REVERT: D   84 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6863 (ptm160)
  outliers start: 20
  outliers final: 15
  residues processed: 77
  average time/residue: 0.7338
  time to fit residues: 59.2415
Evaluate side-chains
  81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   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 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 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 = 0.4388 r_free = 0.4388 target = 0.192279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.166040 restraints weight = 4458.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.49
r_work: 0.4022 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3636  Z= 0.193
  Angle     :  0.816   8.072   4976  Z= 0.418
  Chirality :  0.049   0.165    556
  Planarity :  0.003   0.039    624
  Dihedral  :  6.753  54.793    519
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 34.59 %
    Favored  : 59.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -1.96 (0.35), residues: 468
  helix: -2.69 (0.76), residues: 24
  sheet: -1.29 (0.27), residues: 280
  loop : -0.68 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  75 
 HIS   0.002   0.001   HIS D 127 
 PHE   0.012   0.002   PHE D  29 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.009   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  184)
  hydrogen bonds       : angle       7.25460 (  480)
  covalent geometry    : bond        0.00440 ( 3636)
  covalent geometry    : angle       0.81624 ( 4976)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7077 (m100) cc_final: 0.6293 (m-90)
REVERT: A  101 GLU cc_start: 0.6691 (pp20) cc_final: 0.6248 (pp20)
REVERT: B   79 TRP cc_start: 0.7060 (m100) cc_final: 0.6290 (m-90)
REVERT: B   84 ARG cc_start: 0.7273 (ttm110) cc_final: 0.7068 (ptm160)
REVERT: D   79 TRP cc_start: 0.7028 (m100) cc_final: 0.6360 (m-90)
REVERT: D   84 ARG cc_start: 0.7170 (ttm110) cc_final: 0.6828 (ptm160)
  outliers start: 20
  outliers final: 17
  residues processed: 82
  average time/residue: 0.7431
  time to fit residues: 63.8975
Evaluate side-chains
  86 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  129 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  85 ASN
D  87 HIS
** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.194015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.169496 restraints weight = 4481.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4166 rms_B_bonded: 2.41
r_work: 0.4066 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3636  Z= 0.147
  Angle     :  0.782   8.908   4976  Z= 0.399
  Chirality :  0.046   0.153    556
  Planarity :  0.003   0.042    624
  Dihedral  :  6.375  56.389    519
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 37.21 %
    Favored  : 59.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -1.87 (0.35), residues: 468
  helix: -2.35 (0.82), residues: 24
  sheet: -1.21 (0.27), residues: 280
  loop : -0.70 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  79 
 HIS   0.001   0.000   HIS D  87 
 PHE   0.010   0.002   PHE C  29 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.009   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02973 (  184)
  hydrogen bonds       : angle       7.02143 (  480)
  covalent geometry    : bond        0.00335 ( 3636)
  covalent geometry    : angle       0.78153 ( 4976)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2435.76 seconds
wall clock time: 42 minutes 38.76 seconds (2558.76 seconds total)