Starting phenix.real_space_refine
on Fri May  9 18:52:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hrm_34978/05_2025/8hrm_34978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hrm_34978/05_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_34978/05_2025/8hrm_34978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hrm_34978/05_2025/8hrm_34978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hrm_34978/05_2025/8hrm_34978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hrm_34978/05_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-5687/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: 2.87, per 1000 atoms: 0.80
  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: 0.78
  Conformation dependent library (CDL) restraints added in 407.3 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: 0.43
  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: 1.01

  Time building geometry restraints manager: 0.94 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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.990
  Find NCS groups from input model:        0.110
  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:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.430
-------------------------------------------------------------------------------
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  : 0.353 
Fit side-chains
  outliers start: 14
  outliers final: 9
  residues processed: 81
  average time/residue: 0.5573
  time to fit residues: 47.8610
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  : 0.376 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.172112 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: 0.7475
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  : 0.369 
Fit side-chains
REVERT: A   95 GLN cc_start: 0.8051 (pt0) cc_final: 0.7816 (pt0)
  outliers start: 26
  outliers final: 14
  residues processed: 86
  average time/residue: 0.6268
  time to fit residues: 56.8979
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  : 0.343 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    4.1786

-------------------------------------------------------------------------------
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  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4387 r_free = 0.4387 target = 0.192175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.164342 restraints weight = 4450.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.52
r_work: 0.4005 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066   3636  Z= 0.293
  Angle     :  0.800   6.412   4976  Z= 0.415
  Chirality :  0.049   0.160    556
  Planarity :  0.004   0.046    624
  Dihedral  :  6.609  28.006    519
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  5.34 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  9.01 %
    Allowed  : 26.45 %
    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: -1.60 (0.38), residues: 468
  helix: -2.84 (0.79), residues: 24
  sheet: -1.15 (0.28), residues: 284
  loop : -0.11 (0.54), residues: 160

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   0.013   0.003   PHE B  29 
 TYR   0.015   0.002   TYR B  54 
 ARG   0.011   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  184)
  hydrogen bonds       : angle       7.97281 (  480)
  covalent geometry    : bond        0.00673 ( 3636)
  covalent geometry    : angle       0.79991 ( 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
  95 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B   79 TRP cc_start: 0.7048 (m100) cc_final: 0.6590 (m-90)
  outliers start: 31
  outliers final: 16
  residues processed: 86
  average time/residue: 0.7342
  time to fit residues: 66.1031
Evaluate side-chains
  76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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   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   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:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0870
   chunk 3 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.9564

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.193209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.164655 restraints weight = 4520.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.64
r_work: 0.4001 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   3636  Z= 0.228
  Angle     :  0.740   6.442   4976  Z= 0.386
  Chirality :  0.048   0.158    556
  Planarity :  0.004   0.052    624
  Dihedral  :  6.471  27.573    519
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  8.72 %
    Allowed  : 27.33 %
    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: -1.68 (0.37), residues: 468
  helix: -2.82 (0.78), residues: 24
  sheet: -1.08 (0.28), residues: 280
  loop : -0.49 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  92 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.012   0.002   PHE D  29 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.012   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  184)
  hydrogen bonds       : angle       7.70401 (  480)
  covalent geometry    : bond        0.00522 ( 3636)
  covalent geometry    : angle       0.74031 ( 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
  91 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.8299 (mm) cc_final: 0.8086 (mp)
REVERT: B   25 LEU cc_start: 0.8268 (mm) cc_final: 0.8065 (mp)
  outliers start: 30
  outliers final: 17
  residues processed: 84
  average time/residue: 0.7406
  time to fit residues: 65.2027
Evaluate side-chains
  79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 15 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0980
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.4453 r_free = 0.4453 target = 0.198000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.172348 restraints weight = 4497.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 2.53
r_work: 0.4097 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3636  Z= 0.119
  Angle     :  0.658   6.356   4976  Z= 0.337
  Chirality :  0.043   0.149    556
  Planarity :  0.003   0.031    624
  Dihedral  :  5.748  27.498    519
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 30.81 %
    Favored  : 62.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.48 (0.37), residues: 468
  helix: -2.28 (0.87), residues: 24
  sheet: -0.91 (0.27), residues: 280
  loop : -0.52 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  92 
 HIS   0.001   0.001   HIS D  87 
 PHE   0.008   0.001   PHE A  29 
 TYR   0.007   0.001   TYR C  54 
 ARG   0.006   0.001   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02867 (  184)
  hydrogen bonds       : angle       7.23904 (  480)
  covalent geometry    : bond        0.00260 ( 3636)
  covalent geometry    : angle       0.65844 ( 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
  92 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7092 (m100) cc_final: 0.6616 (m-90)
REVERT: A   95 GLN cc_start: 0.8050 (pt0) cc_final: 0.7827 (pt0)
REVERT: B   79 TRP cc_start: 0.7199 (m100) cc_final: 0.6698 (m-90)
REVERT: B   95 GLN cc_start: 0.8070 (pt0) cc_final: 0.7869 (pt0)
REVERT: D   79 TRP cc_start: 0.7090 (m100) cc_final: 0.6480 (m-90)
  outliers start: 23
  outliers final: 14
  residues processed: 82
  average time/residue: 0.6221
  time to fit residues: 53.8444
Evaluate side-chains
  76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  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   28 THR
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  129 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 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 = 0.4398 r_free = 0.4398 target = 0.192672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.166083 restraints weight = 4562.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 2.53
r_work: 0.4027 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3636  Z= 0.234
  Angle     :  0.756   6.719   4976  Z= 0.392
  Chirality :  0.048   0.146    556
  Planarity :  0.004   0.036    624
  Dihedral  :  6.696  45.328    518
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 30.52 %
    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: -1.64 (0.37), residues: 468
  helix: -2.63 (0.78), residues: 24
  sheet: -1.07 (0.28), residues: 280
  loop : -0.46 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.004   0.002   HIS A  87 
 PHE   0.013   0.002   PHE A  29 
 TYR   0.011   0.001   TYR C  54 
 ARG   0.008   0.001   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  184)
  hydrogen bonds       : angle       7.43655 (  480)
  covalent geometry    : bond        0.00535 ( 3636)
  covalent geometry    : angle       0.75585 ( 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
  90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7096 (m100) cc_final: 0.6292 (m-90)
REVERT: D   79 TRP cc_start: 0.7017 (m100) cc_final: 0.6344 (m-90)
REVERT: D   84 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6924 (ptm160)
  outliers start: 25
  outliers final: 18
  residues processed: 81
  average time/residue: 0.6846
  time to fit residues: 58.2391
Evaluate side-chains
  77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   39 LEU
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   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   52 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  131 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 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 = 0.4399 r_free = 0.4399 target = 0.193067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.166634 restraints weight = 4455.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 2.51
r_work: 0.4034 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3636  Z= 0.197
  Angle     :  0.727   6.155   4976  Z= 0.377
  Chirality :  0.047   0.144    556
  Planarity :  0.003   0.040    624
  Dihedral  :  6.275  45.034    517
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.27 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 31.40 %
    Favored  : 61.34 %
  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: -1.76 (0.36), residues: 468
  helix: -2.47 (0.82), residues: 24
  sheet: -1.15 (0.28), residues: 280
  loop : -0.58 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  75 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.012   0.002   PHE D  29 
 TYR   0.009   0.001   TYR C  54 
 ARG   0.010   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03111 (  184)
  hydrogen bonds       : angle       7.29893 (  480)
  covalent geometry    : bond        0.00450 ( 3636)
  covalent geometry    : angle       0.72742 ( 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
  86 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7103 (m100) cc_final: 0.6327 (m-90)
REVERT: B   84 ARG cc_start: 0.7346 (ttm110) cc_final: 0.7015 (ptm160)
REVERT: D   79 TRP cc_start: 0.7001 (m100) cc_final: 0.6323 (m-90)
REVERT: D   84 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6894 (ptm160)
  outliers start: 25
  outliers final: 15
  residues processed: 77
  average time/residue: 0.6416
  time to fit residues: 52.0832
Evaluate side-chains
  71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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   52 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  131 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:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 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 = 0.4373 r_free = 0.4373 target = 0.190854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.163439 restraints weight = 4519.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 2.48
r_work: 0.3993 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   3636  Z= 0.299
  Angle     :  0.858   6.900   4976  Z= 0.443
  Chirality :  0.051   0.173    556
  Planarity :  0.004   0.036    624
  Dihedral  :  6.476  30.694    516
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  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: -1.98 (0.36), residues: 468
  helix: -2.86 (0.74), residues: 24
  sheet: -1.28 (0.28), residues: 280
  loop : -0.68 (0.47), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  75 
 HIS   0.003   0.002   HIS A  87 
 PHE   0.016   0.003   PHE A  29 
 TYR   0.011   0.002   TYR C  54 
 ARG   0.006   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  184)
  hydrogen bonds       : angle       7.55290 (  480)
  covalent geometry    : bond        0.00687 ( 3636)
  covalent geometry    : angle       0.85786 ( 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
  92 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7074 (m100) cc_final: 0.6441 (m-90)
REVERT: A  101 GLU cc_start: 0.6656 (pp20) cc_final: 0.6235 (pp20)
REVERT: B   79 TRP cc_start: 0.7037 (m100) cc_final: 0.6291 (m-90)
REVERT: B   84 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7010 (ptm160)
REVERT: B  101 GLU cc_start: 0.6734 (pp20) cc_final: 0.6275 (pp20)
REVERT: D   79 TRP cc_start: 0.6961 (m100) cc_final: 0.6386 (m-90)
REVERT: D   84 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6897 (ptm160)
REVERT: D  101 GLU cc_start: 0.6714 (pp20) cc_final: 0.6263 (pp20)
  outliers start: 26
  outliers final: 15
  residues processed: 84
  average time/residue: 0.6893
  time to fit residues: 60.7998
Evaluate side-chains
  80 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    2.4384

-------------------------------------------------------------------------------
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 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 = 0.4384 r_free = 0.4384 target = 0.192117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.165988 restraints weight = 4427.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 2.45
r_work: 0.4020 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2714

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= 0.210
  Angle     :  0.782   7.339   4976  Z= 0.402
  Chirality :  0.049   0.175    556
  Planarity :  0.004   0.041    624
  Dihedral  :  6.185  28.751    516
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.63 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 32.27 %
    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: -2.03 (0.35), residues: 468
  helix: -2.84 (0.73), residues: 24
  sheet: -1.32 (0.27), residues: 280
  loop : -0.73 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.002   0.001   HIS D  87 
 PHE   0.012   0.002   PHE A  29 
 TYR   0.008   0.001   TYR C  54 
 ARG   0.007   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (  184)
  hydrogen bonds       : angle       7.35842 (  480)
  covalent geometry    : bond        0.00483 ( 3636)
  covalent geometry    : angle       0.78188 ( 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  : 0.398 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7111 (m100) cc_final: 0.6358 (m-90)
REVERT: B   79 TRP cc_start: 0.7045 (m100) cc_final: 0.6209 (m-90)
REVERT: B   84 ARG cc_start: 0.7237 (ttm110) cc_final: 0.6951 (ptm160)
REVERT: D   79 TRP cc_start: 0.7011 (m100) cc_final: 0.6323 (m-90)
REVERT: D   84 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6855 (ptm160)
  outliers start: 20
  outliers final: 15
  residues processed: 79
  average time/residue: 0.6702
  time to fit residues: 55.8196
Evaluate side-chains
  79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 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 = 0.4370 r_free = 0.4370 target = 0.191396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.164618 restraints weight = 4468.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4096 rms_B_bonded: 2.45
r_work: 0.3997 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   3636  Z= 0.259
  Angle     :  0.858   8.056   4976  Z= 0.442
  Chirality :  0.051   0.175    556
  Planarity :  0.003   0.038    624
  Dihedral  :  6.410  29.628    516
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.06 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 34.59 %
    Favored  : 60.47 %
  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: -2.16 (0.35), residues: 468
  helix: -2.96 (0.70), residues: 24
  sheet: -1.39 (0.27), residues: 280
  loop : -0.83 (0.45), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.003   0.002   HIS D  87 
 PHE   0.014   0.002   PHE B  29 
 TYR   0.009   0.002   TYR C  54 
 ARG   0.006   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  184)
  hydrogen bonds       : angle       7.44639 (  480)
  covalent geometry    : bond        0.00597 ( 3636)
  covalent geometry    : angle       0.85838 ( 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
  87 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   79 TRP cc_start: 0.7094 (m100) cc_final: 0.6396 (m-90)
REVERT: A   84 ARG cc_start: 0.7316 (mtp180) cc_final: 0.7080 (mtp180)
REVERT: B   79 TRP cc_start: 0.7034 (m100) cc_final: 0.6281 (m-90)
REVERT: B   84 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6952 (ptm160)
REVERT: B  101 GLU cc_start: 0.6768 (pp20) cc_final: 0.6223 (pp20)
REVERT: D   79 TRP cc_start: 0.6988 (m100) cc_final: 0.6330 (m-90)
REVERT: D   84 ARG cc_start: 0.7200 (ttm110) cc_final: 0.6898 (ptm160)
REVERT: D  101 GLU cc_start: 0.6799 (pp20) cc_final: 0.6234 (pp20)
  outliers start: 17
  outliers final: 15
  residues processed: 83
  average time/residue: 0.7277
  time to fit residues: 63.3644
Evaluate side-chains
  83 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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  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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 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 = 0.4367 r_free = 0.4367 target = 0.190607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.163518 restraints weight = 4489.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.49
r_work: 0.3988 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   3636  Z= 0.268
  Angle     :  0.859   8.835   4976  Z= 0.443
  Chirality :  0.051   0.171    556
  Planarity :  0.004   0.053    624
  Dihedral  :  6.469  30.734    516
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 34.59 %
    Favored  : 60.47 %
  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: -2.23 (0.35), residues: 468
  helix: -3.02 (0.69), residues: 24
  sheet: -1.43 (0.27), residues: 280
  loop : -0.88 (0.44), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  75 
 HIS   0.003   0.002   HIS D  87 
 PHE   0.014   0.002   PHE B  29 
 TYR   0.010   0.002   TYR A  54 
 ARG   0.005   0.001   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  184)
  hydrogen bonds       : angle       7.47337 (  480)
  covalent geometry    : bond        0.00617 ( 3636)
  covalent geometry    : angle       0.85880 ( 4976)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2311.28 seconds
wall clock time: 40 minutes 49.24 seconds (2449.24 seconds total)