Starting phenix.real_space_refine
on Fri Aug 22 15:45:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p77_17520/08_2025/8p77_17520.map"
  }
  resolution = 1.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    3313      2.51       5
     N     876      2.21       5
     O    1051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5271
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2281
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 279, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 58
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I73': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I73': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "I"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 58
          Classifications: {'water': 58}
          Link IDs: {None: 57}
    Chain: "J"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 64
          Classifications: {'water': 64}
          Link IDs: {None: 63}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C11AI73 J 401 " occ=0.50
      ... (56 atoms not shown)
      pdb=" O1 BI73 J 401 " occ=0.50
  Time building chain proxies: 1.28, per 1000 atoms: 0.24
  Number of scatterers: 5271
  At special positions: 0
  Unit cell: (84.7875, 93.3375, 67.6875, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1051      8.00
     N     876      7.00
     C    3313      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: 0.46
  Conformation dependent library (CDL) restraints added in 174.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.9% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.513A  pdb=" N   ASN H 273 " --> pdb=" O   GLY H 270 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 286
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.796A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
    Processing helix  chain 'I' and resid 49 through 70
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.908A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.669A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 128
      removed outlier: 3.687A  pdb=" N   ASN I 128 " --> pdb=" O   GLN I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.805A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.738A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 225
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.631A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 262
    Processing helix  chain 'I' and resid 266 through 283
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.298A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.851A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.738A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20
      removed outlier: 7.333A  pdb=" N   LEU J  15 " --> pdb=" O   ARG J  30 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ARG J  30 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   PHE J  17 " --> pdb=" O   LYS J  28 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS J  28 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    273 hydrogen bonds defined for protein.
    768 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: 0.64

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1642
        1.34 -     1.46: 1170
        1.46 -     1.58: 2398
        1.58 -     1.69: 2
        1.69 -     1.81: 49
  Bond restraints: 5261
  Sorted by residual:
  bond pdb=" C3 AI73 J 401 "
       pdb=" N10AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.339  1.517 -0.178 2.00e-02 2.50e+03 7.90e+01
  bond pdb=" C3 BI73 J 401 "
       pdb=" N10BI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.339  1.516 -0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" C5 BI73 J 401 "
       pdb=" N18BI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.480 -0.131 2.00e-02 2.50e+03 4.32e+01
  bond pdb=" C5 AI73 J 401 "
       pdb=" N18AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.480 -0.131 2.00e-02 2.50e+03 4.29e+01
  bond pdb=" N1 AI73 J 401 "
       pdb=" N2 AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.415 -0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 5256 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 6926
        1.45 -     2.89: 140
        2.89 -     4.34: 44
        4.34 -     5.78: 4
        5.78 -     7.23: 7
  Bond angle restraints: 7121
  Sorted by residual:
  angle pdb=" C4 BI73 J 401 "
        pdb=" C3 BI73 J 401 "
        pdb=" N10BI73 J 401 "
      ideal   model   delta    sigma   weight residual
     127.16  119.93    7.23 3.00e+00 1.11e-01 5.81e+00
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  109.65    4.25 1.80e+00 3.09e-01 5.58e+00
  angle pdb=" C4 AI73 J 401 "
        pdb=" C3 AI73 J 401 "
        pdb=" N10AI73 J 401 "
      ideal   model   delta    sigma   weight residual
     127.16  120.17    6.99 3.00e+00 1.11e-01 5.44e+00
  angle pdb=" CB  MET J 189 "
        pdb=" CG  MET J 189 "
        pdb=" SD  MET J 189 "
      ideal   model   delta    sigma   weight residual
     112.70  119.39   -6.69 3.00e+00 1.11e-01 4.97e+00
  angle pdb=" C8 BI73 J 401 "
        pdb=" C9 BI73 J 401 "
        pdb=" N1 BI73 J 401 "
      ideal   model   delta    sigma   weight residual
     113.59  107.37    6.22 3.00e+00 1.11e-01 4.30e+00
  ... (remaining 7116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.84: 2806
       18.84 -    37.68: 287
       37.68 -    56.51: 63
       56.51 -    75.35: 19
       75.35 -    94.19: 6
  Dihedral angle restraints: 3181
    sinusoidal: 1334
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" CA  TYR I  91 "
           pdb=" C   TYR I  91 "
           pdb=" N   LEU I  92 "
           pdb=" CA  LEU I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" C41AI73 J 401 "
           pdb=" C40AI73 J 401 "
           pdb=" N18AI73 J 401 "
           pdb=" C5 AI73 J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     166.20  -99.61  -94.19     1      3.00e+01 1.11e-03 1.14e+01
  dihedral pdb=" CB  GLU J  99 "
           pdb=" CG  GLU J  99 "
           pdb=" CD  GLU J  99 "
           pdb=" OE1 GLU J  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.27   88.27     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 3178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 495
       0.028 -    0.057: 170
       0.057 -    0.085: 72
       0.085 -    0.114: 36
       0.114 -    0.142: 6
  Chirality restraints: 779
  Sorted by residual:
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE J  74 "
            pdb=" N   ILE J  74 "
            pdb=" C   ILE J  74 "
            pdb=" CB  ILE J  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  VAL J 210 "
            pdb=" N   VAL J 210 "
            pdb=" C   VAL J 210 "
            pdb=" CB  VAL J 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 776 not shown)

  Planarity restraints: 905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 139 "    0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO J 140 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO J 140 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO J 140 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP I 193 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.60e+00
        pdb=" C   ASP I 193 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ASP I 193 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE I 194 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J 199 "    0.006 2.00e-02 2.50e+03   1.19e-02 1.42e+00
        pdb=" C   VAL J 199 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   VAL J 199 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY J 200 "    0.007 2.00e-02 2.50e+03
  ... (remaining 902 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 973
        2.76 -     3.30: 5275
        3.30 -     3.83: 10028
        3.83 -     4.37: 11749
        4.37 -     4.90: 19327
  Nonbonded interactions: 47352
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J  97 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   HOH J 514 "
            pdb=" O   HOH J 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE J 295 "
            pdb=" O   HOH J 502 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   HOH I 403 "
            pdb=" O   HOH I 445 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLU I 145 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.277 3.040
  ... (remaining 47347 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             5.060
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     6.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:9.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.178   5261  Z= 0.305
  Angle     :  0.583   7.229   7121  Z= 0.275
  Chirality :  0.039   0.142    779
  Planarity :  0.004   0.035    905
  Dihedral  : 16.680  94.189   1985
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.98 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.34), residues: 618
  helix:  2.07 (0.29), residues: 339
  sheet:  1.40 (1.58), residues: 10
  loop :  0.48 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 268 
 TYR   0.016   0.002   TYR I  60 
 PHE   0.014   0.002   PHE I 110 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.003   0.001   HIS I 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 5261)
  covalent geometry    : angle       0.58315 ( 7121)
  hydrogen bonds       : bond        0.12745 (  273)
  hydrogen bonds       : angle       5.92106 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.135 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 106
  average time/residue: 0.6088
  time to fit residues: 66.7997
Evaluate side-chains
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  290 SER
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0870
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.172114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144931 restraints weight = 20072.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.14
r_work: 0.3674 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.0720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5261  Z= 0.160
  Angle     :  0.576   6.228   7121  Z= 0.298
  Chirality :  0.042   0.142    779
  Planarity :  0.005   0.034    905
  Dihedral  :  8.290  93.306    730
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.44 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.34), residues: 618
  helix:  1.93 (0.28), residues: 345
  sheet:  2.15 (1.24), residues: 15
  loop :  0.38 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 268 
 TYR   0.022   0.002   TYR I  91 
 PHE   0.015   0.002   PHE J 295 
 TRP   0.012   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 5261)
  covalent geometry    : angle       0.57579 ( 7121)
  hydrogen bonds       : bond        0.05374 (  273)
  hydrogen bonds       : angle       4.86394 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.210 
Fit side-chains
REVERT: J   92 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7444 (m-30)
  outliers start: 8
  outliers final: 3
  residues processed: 108
  average time/residue: 0.6110
  time to fit residues: 68.3237
Evaluate side-chains
  103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.173738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.147042 restraints weight = 17444.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 1.98
r_work: 0.3706 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5261  Z= 0.119
  Angle     :  0.509   5.922   7121  Z= 0.264
  Chirality :  0.040   0.139    779
  Planarity :  0.004   0.035    905
  Dihedral  :  7.637  92.599    724
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.54 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.34), residues: 618
  helix:  2.04 (0.28), residues: 346
  sheet:  2.54 (1.31), residues: 15
  loop :  0.56 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 268 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.012   0.002   PHE J 295 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5261)
  covalent geometry    : angle       0.50942 ( 7121)
  hydrogen bonds       : bond        0.04616 (  273)
  hydrogen bonds       : angle       4.59784 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.215 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5175 (mmmt)
REVERT: J   92 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7347 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 108
  average time/residue: 0.6419
  time to fit residues: 71.6654
Evaluate side-chains
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
** J 129 HIS ** 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 = 0.4141 r_free = 0.4141 target = 0.172756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146014 restraints weight = 17701.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.00
r_work: 0.3692 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.0833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.140
  Angle     :  0.539   6.076   7121  Z= 0.279
  Chirality :  0.041   0.143    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.612  92.090    724
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.36 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.34), residues: 618
  helix:  2.06 (0.28), residues: 340
  sheet:  2.47 (1.28), residues: 15
  loop :  0.57 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 268 
 TYR   0.021   0.002   TYR I  91 
 PHE   0.014   0.002   PHE J 295 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5261)
  covalent geometry    : angle       0.53870 ( 7121)
  hydrogen bonds       : bond        0.04900 (  273)
  hydrogen bonds       : angle       4.62112 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.167 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5175 (mmmt)
REVERT: J   92 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7421 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 111
  average time/residue: 0.6134
  time to fit residues: 70.3711
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 28 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0270
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
** J 129 HIS ** 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 = 0.4164 r_free = 0.4164 target = 0.175161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148819 restraints weight = 16717.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.01
r_work: 0.3731 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5261  Z= 0.104
  Angle     :  0.488   5.645   7121  Z= 0.252
  Chirality :  0.039   0.137    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.359  91.745    724
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.08 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.35), residues: 618
  helix:  2.28 (0.28), residues: 340
  sheet:  2.63 (1.30), residues: 15
  loop :  0.64 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 268 
 TYR   0.017   0.002   TYR I  91 
 PHE   0.013   0.001   PHE I 110 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5261)
  covalent geometry    : angle       0.48802 ( 7121)
  hydrogen bonds       : bond        0.04165 (  273)
  hydrogen bonds       : angle       4.40954 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.228 
Fit side-chains
REVERT: I  141 GLU cc_start: 0.7564 (tp30) cc_final: 0.7336 (tp30)
REVERT: J   42 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5102 (mmmt)
REVERT: J   92 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7249 (m-30)
  outliers start: 13
  outliers final: 5
  residues processed: 111
  average time/residue: 0.6237
  time to fit residues: 71.7152
Evaluate side-chains
  108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.174031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.147186 restraints weight = 20326.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 2.14
r_work: 0.3705 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.118
  Angle     :  0.511   5.917   7121  Z= 0.263
  Chirality :  0.040   0.138    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.290  91.496    723
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.52 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.35), residues: 618
  helix:  2.24 (0.28), residues: 340
  sheet:  2.47 (1.29), residues: 15
  loop :  0.66 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 268 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.013   0.002   PHE J  81 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5261)
  covalent geometry    : angle       0.51099 ( 7121)
  hydrogen bonds       : bond        0.04449 (  273)
  hydrogen bonds       : angle       4.42895 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.176 
Fit side-chains
REVERT: I  141 GLU cc_start: 0.7592 (tp30) cc_final: 0.7341 (tp30)
REVERT: I  268 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6008 (pm20)
REVERT: J   42 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5112 (mmmt)
REVERT: J   92 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7341 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 111
  average time/residue: 0.5680
  time to fit residues: 65.2868
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0030
   chunk 7 optimal weight:    0.0010
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.174039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.146642 restraints weight = 19453.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.18
r_work: 0.3703 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.0935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.121
  Angle     :  0.515   5.862   7121  Z= 0.265
  Chirality :  0.040   0.138    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.256  91.200    723
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.98 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.34), residues: 618
  helix:  2.21 (0.28), residues: 340
  sheet:  2.43 (1.30), residues: 15
  loop :  0.66 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 268 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.012   0.002   PHE J 295 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5261)
  covalent geometry    : angle       0.51479 ( 7121)
  hydrogen bonds       : bond        0.04497 (  273)
  hydrogen bonds       : angle       4.43898 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.203 
Fit side-chains
REVERT: I  141 GLU cc_start: 0.7590 (tp30) cc_final: 0.7336 (tp30)
REVERT: J   42 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5127 (mmmt)
REVERT: J   92 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7347 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 110
  average time/residue: 0.5211
  time to fit residues: 59.6073
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.173515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.146119 restraints weight = 19361.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.18
r_work: 0.3696 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.129
  Angle     :  0.532   5.940   7121  Z= 0.273
  Chirality :  0.040   0.140    779
  Planarity :  0.004   0.033    905
  Dihedral  :  7.245  90.705    723
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.98 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.34), residues: 618
  helix:  2.18 (0.28), residues: 340
  sheet:  2.38 (1.30), residues: 15
  loop :  0.65 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 268 
 TYR   0.020   0.002   TYR I  91 
 PHE   0.015   0.002   PHE J  81 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5261)
  covalent geometry    : angle       0.53154 ( 7121)
  hydrogen bonds       : bond        0.04656 (  273)
  hydrogen bonds       : angle       4.46267 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.207 
Fit side-chains
REVERT: I  124 GLN cc_start: 0.7068 (pt0) cc_final: 0.6111 (tp-100)
REVERT: I  141 GLU cc_start: 0.7576 (tp30) cc_final: 0.7303 (tp30)
REVERT: I  268 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5856 (pm20)
REVERT: J   42 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5123 (mmmt)
REVERT: J   92 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7379 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 108
  average time/residue: 0.6256
  time to fit residues: 69.9697
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.174375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.147121 restraints weight = 19065.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 2.14
r_work: 0.3705 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.118
  Angle     :  0.520   5.830   7121  Z= 0.266
  Chirality :  0.040   0.139    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.193  90.408    723
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.52 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.35), residues: 618
  helix:  2.21 (0.28), residues: 340
  sheet:  2.41 (1.33), residues: 15
  loop :  0.69 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 268 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.012   0.002   PHE J  91 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5261)
  covalent geometry    : angle       0.52027 ( 7121)
  hydrogen bonds       : bond        0.04440 (  273)
  hydrogen bonds       : angle       4.42796 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.195 
Fit side-chains
REVERT: I  141 GLU cc_start: 0.7591 (tp30) cc_final: 0.7356 (tp30)
REVERT: I  268 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5777 (pm20)
REVERT: J   42 LYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5041 (mmmt)
REVERT: J   92 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7358 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6020
  time to fit residues: 66.7621
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0570
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.3502

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.172413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.145413 restraints weight = 19162.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.13
r_work: 0.3685 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5261  Z= 0.159
  Angle     :  0.578   6.172   7121  Z= 0.297
  Chirality :  0.042   0.143    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.334  89.908    723
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.06 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.34), residues: 618
  helix:  2.02 (0.28), residues: 340
  sheet:  2.30 (1.31), residues: 15
  loop :  0.63 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 268 
 TYR   0.022   0.002   TYR I  91 
 PHE   0.019   0.002   PHE J  81 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.005   0.001   HIS I 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5261)
  covalent geometry    : angle       0.57796 ( 7121)
  hydrogen bonds       : bond        0.05059 (  273)
  hydrogen bonds       : angle       4.58623 (  768)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.130 
Fit side-chains
REVERT: I  124 GLN cc_start: 0.7095 (pt0) cc_final: 0.6158 (tp-100)
REVERT: I  268 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5831 (pm20)
REVERT: J   92 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7443 (m-30)
  outliers start: 8
  outliers final: 4
  residues processed: 107
  average time/residue: 0.6156
  time to fit residues: 68.2673
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.172360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145724 restraints weight = 16799.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.97
r_work: 0.3686 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.143
  Angle     :  0.562   7.196   7121  Z= 0.288
  Chirality :  0.041   0.141    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.326  89.519    723
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 16.06 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.34), residues: 618
  helix:  1.99 (0.28), residues: 340
  sheet:  2.45 (1.34), residues: 15
  loop :  0.62 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 268 
 TYR   0.021   0.002   TYR I  91 
 PHE   0.013   0.002   PHE J 295 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5261)
  covalent geometry    : angle       0.56201 ( 7121)
  hydrogen bonds       : bond        0.04846 (  273)
  hydrogen bonds       : angle       4.53677 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3315.12 seconds
wall clock time: 56 minutes 55.39 seconds (3415.39 seconds total)