Starting phenix.real_space_refine
on Wed Jun  4 09:54:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w3t_32293/06_2025/7w3t_32293.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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       3      5.16       5
     C     915      2.51       5
     N     241      2.21       5
     O     296      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 1455
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1360
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 13, 'TRANS': 162}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.95, per 1000 atoms: 1.34
  Number of scatterers: 1455
  At special positions: 0
  Unit cell: (66.843, 46.684, 55.172, 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       3     16.00
     O     296      8.00
     N     241      7.00
     C     915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  67 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN B 186 "
      " NAG B1000 " - " ASN B  82 "
      " NAG B1001 " - " ASN B 106 "
      " NAG B1002 " - " ASN B 117 "
      " NAG B1003 " - " ASN B 152 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 178.0 milliseconds
  

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  330

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 3 sheets defined
      27.8% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 41
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 3.574A  pdb=" N   GLN B  93 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU B  94 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 90 through 94'
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 3.819A  pdb=" N   LEU B 115 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 142
      removed outlier: 3.501A  pdb=" N   LEU B 142 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 166
      removed outlier: 3.565A  pdb=" N   VAL B 166 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.503A  pdb=" N   PHE B 189 " --> pdb=" O   ASN B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 197
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43
      removed outlier: 5.402A  pdb=" N   GLY B  85 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66
      removed outlier: 6.383A  pdb=" N   VAL B  76 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU B 100 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU B 124 " --> pdb=" O   ARG B 149 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ASN B 151 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 148 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 175 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158
      removed outlier: 6.452A  pdb=" N   GLY B 157 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    27 hydrogen bonds defined for protein.
    39 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: 0.31

  Time building geometry restraints manager: 0.59 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: 475
        1.34 -     1.46: 267
        1.46 -     1.57: 735
        1.57 -     1.69: 0
        1.69 -     1.81: 4
  Bond restraints: 1481
  Sorted by residual:
  bond pdb=" C1  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.75e+00
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C1  BMA A   3 "
       pdb=" C2  BMA A   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.545 -0.026 2.00e-02 2.50e+03 1.65e+00
  bond pdb=" C1  NAG B1003 "
       pdb=" O5  NAG B1003 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.55e+00
  bond pdb=" C1  NAG B1000 "
       pdb=" O5  NAG B1000 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.46e+00
  ... (remaining 1476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 1908
        1.43 -     2.86: 103
        2.86 -     4.29: 10
        4.29 -     5.72: 6
        5.72 -     7.15: 2
  Bond angle restraints: 2029
  Sorted by residual:
  angle pdb=" CA  PRO B 134 "
        pdb=" C   PRO B 134 "
        pdb=" N   ILE B 135 "
      ideal   model   delta    sigma   weight residual
     114.74  116.95   -2.21 1.03e+00 9.43e-01 4.62e+00
  angle pdb=" C3  BMA A   3 "
        pdb=" C2  BMA A   3 "
        pdb=" O2  BMA A   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.58    6.37 3.00e+00 1.11e-01 4.50e+00
  angle pdb=" CA  LEU B 162 "
        pdb=" CB  LEU B 162 "
        pdb=" CG  LEU B 162 "
      ideal   model   delta    sigma   weight residual
     116.30  123.45   -7.15 3.50e+00 8.16e-02 4.17e+00
  angle pdb=" CA  CYS B  60 "
        pdb=" CB  CYS B  60 "
        pdb=" SG  CYS B  60 "
      ideal   model   delta    sigma   weight residual
     114.40  109.82    4.58 2.30e+00 1.89e-01 3.96e+00
  angle pdb=" C   LYS B 144 "
        pdb=" N   LEU B 145 "
        pdb=" CA  LEU B 145 "
      ideal   model   delta    sigma   weight residual
     122.74  119.46    3.28 1.82e+00 3.02e-01 3.26e+00
  ... (remaining 2024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.50: 897
       21.50 -    43.00: 71
       43.00 -    64.50: 8
       64.50 -    86.00: 8
       86.00 -   107.50: 4
  Dihedral angle restraints: 988
    sinusoidal: 480
      harmonic: 508
  Sorted by residual:
  dihedral pdb=" CB  CYS B  60 "
           pdb=" SG  CYS B  60 "
           pdb=" SG  CYS B  67 "
           pdb=" CB  CYS B  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.69  -39.69     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" O4  BMA A   3 "
           pdb=" C4  BMA A   3 "
           pdb=" C5  BMA A   3 "
           pdb=" O5  BMA A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.79  107.50     1      3.00e+01 1.11e-03 1.39e+01
  dihedral pdb=" C3  BMA A   3 "
           pdb=" C4  BMA A   3 "
           pdb=" C5  BMA A   3 "
           pdb=" O5  BMA A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -57.71  105.33     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 209
       0.055 -    0.110: 44
       0.110 -    0.165: 7
       0.165 -    0.220: 3
       0.220 -    0.275: 1
  Chirality restraints: 264
  Sorted by residual:
  chirality pdb=" C5  BMA A   3 "
            pdb=" C4  BMA A   3 "
            pdb=" C6  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C1  NAG B1000 "
            pdb=" ND2 ASN B  82 "
            pdb=" C2  NAG B1000 "
            pdb=" O5  NAG B1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 7.94e-01
  chirality pdb=" C1  NAG B1001 "
            pdb=" ND2 ASN B 106 "
            pdb=" C2  NAG B1001 "
            pdb=" O5  NAG B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 261 not shown)

  Planarity restraints: 263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  62 "    0.018 2.00e-02 2.50e+03   1.86e-02 8.63e+00
        pdb=" CG  TRP B  62 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  62 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  62 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  62 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  62 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  62 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  62 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  62 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  62 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 159 "   -0.026 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO B 160 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 160 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 160 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  58 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO B  59 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  59 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  59 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 260 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 321
        2.79 -     3.32: 1407
        3.32 -     3.84: 2237
        3.84 -     4.37: 2594
        4.37 -     4.90: 4242
  Nonbonded interactions: 10801
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  68 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LEU B 162 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   GLY B 187 "
            pdb=" OG  SER B 190 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU B 145 "
            pdb=" OG  SER B 168 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   GLY B  85 "
            pdb=" N   SER B 108 "
     model   vdw
     2.389 3.120
  ... (remaining 10796 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.990
  Find NCS groups from input model:        0.010
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   1489  Z= 0.207
  Angle     :  0.762   7.147   2052  Z= 0.343
  Chirality :  0.052   0.275    264
  Planarity :  0.006   0.040    258
  Dihedral  : 17.978 107.496    655
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.63), residues: 174
  helix: -2.58 (0.70), residues: 44
  sheet: -2.90 (0.90), residues: 28
  loop : -1.17 (0.65), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.006   TRP B  62 
 HIS   0.001   0.001   HIS B  64 
 PHE   0.007   0.001   PHE B 147 
 TYR   0.012   0.002   TYR B 127 
 ARG   0.001   0.000   ARG B 130 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    5)
  link_NAG-ASN         : angle       2.29063 (   15)
  link_BETA1-4         : bond        0.00303 (    2)
  link_BETA1-4         : angle       1.24640 (    6)
  hydrogen bonds       : bond        0.24601 (   27)
  hydrogen bonds       : angle       7.22475 (   39)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       3.14491 (    2)
  covalent geometry    : bond        0.00439 ( 1481)
  covalent geometry    : angle       0.73068 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8180 (m110) cc_final: 0.7686 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1131
  time to fit residues: 5.3973
Evaluate side-chains
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.126141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105743 restraints weight = 2208.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109191 restraints weight = 1244.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.111644 restraints weight = 828.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   1489  Z= 0.193
  Angle     :  0.766   9.220   2052  Z= 0.350
  Chirality :  0.052   0.220    264
  Planarity :  0.006   0.035    258
  Dihedral  : 11.247  54.768    329
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 15.00 %
    Favored  : 84.38 %
  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: -2.99 (0.62), residues: 174
  helix: -2.80 (0.69), residues: 44
  sheet: -2.79 (0.88), residues: 29
  loop : -1.26 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B  62 
 HIS   0.003   0.002   HIS B  64 
 PHE   0.014   0.002   PHE B 147 
 TYR   0.014   0.002   TYR B 103 
 ARG   0.003   0.001   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    5)
  link_NAG-ASN         : angle       2.23117 (   15)
  link_BETA1-4         : bond        0.00221 (    2)
  link_BETA1-4         : angle       2.57735 (    6)
  hydrogen bonds       : bond        0.05021 (   27)
  hydrogen bonds       : angle       6.49476 (   39)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       3.61134 (    2)
  covalent geometry    : bond        0.00442 ( 1481)
  covalent geometry    : angle       0.72393 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8180 (m110) cc_final: 0.7671 (t0)
REVERT: B  127 TYR cc_start: 0.8739 (p90) cc_final: 0.8498 (p90)
REVERT: B  161 MET cc_start: 0.5711 (mmp) cc_final: 0.5353 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 43
  average time/residue: 0.1082
  time to fit residues: 5.4701
Evaluate side-chains
  43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0570
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.103696 restraints weight = 2219.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107274 restraints weight = 1241.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109676 restraints weight = 824.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   1489  Z= 0.209
  Angle     :  0.729   6.882   2052  Z= 0.346
  Chirality :  0.052   0.225    264
  Planarity :  0.006   0.041    258
  Dihedral  :  8.313  52.945    329
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.25 %
    Favored  : 80.62 %
  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: -3.05 (0.62), residues: 174
  helix: -2.96 (0.68), residues: 44
  sheet: -2.84 (0.88), residues: 29
  loop : -1.25 (0.65), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B  62 
 HIS   0.003   0.002   HIS B  64 
 PHE   0.013   0.002   PHE B 147 
 TYR   0.013   0.002   TYR B 103 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    5)
  link_NAG-ASN         : angle       2.07740 (   15)
  link_BETA1-4         : bond        0.00137 (    2)
  link_BETA1-4         : angle       2.50181 (    6)
  hydrogen bonds       : bond        0.04780 (   27)
  hydrogen bonds       : angle       6.30330 (   39)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       3.08074 (    2)
  covalent geometry    : bond        0.00474 ( 1481)
  covalent geometry    : angle       0.69108 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8206 (m110) cc_final: 0.7711 (t0)
REVERT: B  127 TYR cc_start: 0.8826 (p90) cc_final: 0.8497 (p90)
REVERT: B  161 MET cc_start: 0.5787 (mmp) cc_final: 0.5306 (mmp)
  outliers start: 5
  outliers final: 2
  residues processed: 44
  average time/residue: 0.0985
  time to fit residues: 5.0976
Evaluate side-chains
  44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 16 optimal weight:    0.0470
   chunk 14 optimal weight:    0.0980
   chunk 12 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 4 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.2056

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106877 restraints weight = 2158.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.110421 restraints weight = 1195.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112875 restraints weight = 789.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   1489  Z= 0.123
  Angle     :  0.659   5.783   2052  Z= 0.319
  Chirality :  0.049   0.217    264
  Planarity :  0.005   0.034    258
  Dihedral  :  7.164  53.865    329
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.25 %
    Favored  : 78.75 %
  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: -2.95 (0.63), residues: 174
  helix: -2.73 (0.71), residues: 44
  sheet: -2.93 (0.96), residues: 27
  loop : -1.25 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  62 
 HIS   0.001   0.001   HIS B  64 
 PHE   0.008   0.001   PHE B 147 
 TYR   0.007   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    5)
  link_NAG-ASN         : angle       1.93492 (   15)
  link_BETA1-4         : bond        0.00353 (    2)
  link_BETA1-4         : angle       2.04187 (    6)
  hydrogen bonds       : bond        0.03934 (   27)
  hydrogen bonds       : angle       5.79307 (   39)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       2.51386 (    2)
  covalent geometry    : bond        0.00284 ( 1481)
  covalent geometry    : angle       0.62722 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8118 (m110) cc_final: 0.7682 (t0)
REVERT: B  127 TYR cc_start: 0.8763 (p90) cc_final: 0.8423 (p90)
REVERT: B  161 MET cc_start: 0.5757 (mmp) cc_final: 0.5185 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1063
  time to fit residues: 4.8429
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0000
   chunk 6 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 7 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.105121 restraints weight = 2181.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.108658 restraints weight = 1224.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111082 restraints weight = 815.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   1489  Z= 0.152
  Angle     :  0.653   5.845   2052  Z= 0.317
  Chirality :  0.049   0.217    264
  Planarity :  0.005   0.030    258
  Dihedral  :  6.919  54.067    329
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.25 %
    Favored  : 78.75 %
  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: -2.90 (0.64), residues: 174
  helix: -2.72 (0.71), residues: 44
  sheet: -2.88 (0.98), residues: 27
  loop : -1.21 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B  62 
 HIS   0.002   0.001   HIS B  64 
 PHE   0.010   0.001   PHE B 147 
 TYR   0.010   0.002   TYR B 103 
 ARG   0.001   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    5)
  link_NAG-ASN         : angle       1.87159 (   15)
  link_BETA1-4         : bond        0.00241 (    2)
  link_BETA1-4         : angle       1.85858 (    6)
  hydrogen bonds       : bond        0.04006 (   27)
  hydrogen bonds       : angle       5.79228 (   39)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       3.08109 (    2)
  covalent geometry    : bond        0.00356 ( 1481)
  covalent geometry    : angle       0.62154 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.161 
Fit side-chains
REVERT: B   41 ASN cc_start: 0.8132 (m110) cc_final: 0.7673 (t0)
REVERT: B  161 MET cc_start: 0.5772 (mmp) cc_final: 0.5166 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1077
  time to fit residues: 5.0861
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 1 optimal weight:    0.2980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 0 optimal weight:    0.1980
   chunk 3 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
** B 153 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.124394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.103501 restraints weight = 2197.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.107158 restraints weight = 1199.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109596 restraints weight = 791.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   1489  Z= 0.130
  Angle     :  0.637   6.721   2052  Z= 0.309
  Chirality :  0.048   0.222    264
  Planarity :  0.004   0.029    258
  Dihedral  :  6.682  54.399    329
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.62 %
    Favored  : 77.50 %
  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: -2.76 (0.65), residues: 174
  helix: -2.58 (0.74), residues: 44
  sheet: -2.85 (0.99), residues: 27
  loop : -1.11 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  62 
 HIS   0.002   0.001   HIS B  64 
 PHE   0.008   0.001   PHE B 147 
 TYR   0.007   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00429 (    5)
  link_NAG-ASN         : angle       1.97604 (   15)
  link_BETA1-4         : bond        0.00285 (    2)
  link_BETA1-4         : angle       1.65179 (    6)
  hydrogen bonds       : bond        0.03673 (   27)
  hydrogen bonds       : angle       5.62464 (   39)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       2.69515 (    2)
  covalent geometry    : bond        0.00305 ( 1481)
  covalent geometry    : angle       0.60532 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8472 (m) cc_final: 0.8220 (t)
REVERT: B   41 ASN cc_start: 0.8134 (m110) cc_final: 0.7618 (t0)
REVERT: B  161 MET cc_start: 0.5758 (mmp) cc_final: 0.5127 (mmp)
REVERT: B  162 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7191 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1048
  time to fit residues: 5.0820
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  162 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0170
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.121874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101470 restraints weight = 2274.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105176 restraints weight = 1239.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107543 restraints weight = 809.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   1489  Z= 0.244
  Angle     :  0.713   6.153   2052  Z= 0.345
  Chirality :  0.052   0.240    264
  Planarity :  0.005   0.034    258
  Dihedral  :  6.907  53.849    329
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.62 %
    Favored  : 77.50 %
  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: -3.01 (0.64), residues: 174
  helix: -2.94 (0.68), residues: 44
  sheet: -2.87 (0.99), residues: 27
  loop : -1.24 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B  62 
 HIS   0.003   0.002   HIS B  64 
 PHE   0.015   0.002   PHE B 147 
 TYR   0.014   0.003   TYR B 103 
 ARG   0.002   0.001   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    5)
  link_NAG-ASN         : angle       2.06231 (   15)
  link_BETA1-4         : bond        0.00179 (    2)
  link_BETA1-4         : angle       1.81363 (    6)
  hydrogen bonds       : bond        0.04462 (   27)
  hydrogen bonds       : angle       6.05466 (   39)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       3.40905 (    2)
  covalent geometry    : bond        0.00550 ( 1481)
  covalent geometry    : angle       0.67957 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8197 (m110) cc_final: 0.7686 (t0)
REVERT: B  161 MET cc_start: 0.5898 (mmp) cc_final: 0.5332 (mmp)
REVERT: B  162 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7336 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 40
  average time/residue: 0.1094
  time to fit residues: 5.1446
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  162 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 10 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.123344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.103047 restraints weight = 2218.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106718 restraints weight = 1208.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.109020 restraints weight = 791.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   1489  Z= 0.143
  Angle     :  0.651   5.494   2052  Z= 0.313
  Chirality :  0.049   0.227    264
  Planarity :  0.005   0.030    258
  Dihedral  :  6.715  54.437    329
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.25 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.65), residues: 174
  helix: -2.76 (0.70), residues: 44
  sheet: -2.82 (1.02), residues: 27
  loop : -1.13 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B  62 
 HIS   0.002   0.001   HIS B  64 
 PHE   0.010   0.002   PHE B 147 
 TYR   0.009   0.002   TYR B 103 
 ARG   0.001   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00425 (    5)
  link_NAG-ASN         : angle       2.03244 (   15)
  link_BETA1-4         : bond        0.00256 (    2)
  link_BETA1-4         : angle       1.58653 (    6)
  hydrogen bonds       : bond        0.03778 (   27)
  hydrogen bonds       : angle       5.69290 (   39)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       2.68362 (    2)
  covalent geometry    : bond        0.00335 ( 1481)
  covalent geometry    : angle       0.61964 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8147 (m110) cc_final: 0.7651 (t0)
REVERT: B  161 MET cc_start: 0.5824 (mmp) cc_final: 0.5273 (mmp)
  outliers start: 3
  outliers final: 2
  residues processed: 40
  average time/residue: 0.1046
  time to fit residues: 4.9403
Evaluate side-chains
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 GLU
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 0 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
B 178 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.122580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.102345 restraints weight = 2237.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.106037 restraints weight = 1214.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.108399 restraints weight = 792.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   1489  Z= 0.173
  Angle     :  0.661   5.499   2052  Z= 0.320
  Chirality :  0.050   0.225    264
  Planarity :  0.005   0.031    258
  Dihedral  :  6.729  54.001    329
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 21.25 %
    Favored  : 77.50 %
  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: -2.88 (0.65), residues: 174
  helix: -2.83 (0.70), residues: 44
  sheet: -2.74 (1.04), residues: 27
  loop : -1.18 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.005   TRP B  62 
 HIS   0.003   0.002   HIS B  64 
 PHE   0.012   0.002   PHE B 147 
 TYR   0.011   0.002   TYR B 103 
 ARG   0.001   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00374 (    5)
  link_NAG-ASN         : angle       2.02992 (   15)
  link_BETA1-4         : bond        0.00192 (    2)
  link_BETA1-4         : angle       1.64565 (    6)
  hydrogen bonds       : bond        0.03977 (   27)
  hydrogen bonds       : angle       5.87816 (   39)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       2.90533 (    2)
  covalent geometry    : bond        0.00400 ( 1481)
  covalent geometry    : angle       0.62822 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8170 (m110) cc_final: 0.7675 (t0)
REVERT: B  161 MET cc_start: 0.5872 (mmp) cc_final: 0.5313 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1053
  time to fit residues: 4.8241
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 GLU
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.122174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.101859 restraints weight = 2192.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.105479 restraints weight = 1213.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107855 restraints weight = 801.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   1489  Z= 0.239
  Angle     :  0.717   6.203   2052  Z= 0.348
  Chirality :  0.052   0.231    264
  Planarity :  0.005   0.032    258
  Dihedral  :  6.916  53.954    329
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 22.50 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.63), residues: 174
  helix: -3.08 (0.66), residues: 44
  sheet: -3.17 (0.98), residues: 26
  loop : -1.23 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.006   TRP B  62 
 HIS   0.003   0.002   HIS B  64 
 PHE   0.015   0.002   PHE B 147 
 TYR   0.014   0.003   TYR B 103 
 ARG   0.002   0.001   ARG B 110 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    5)
  link_NAG-ASN         : angle       2.08189 (   15)
  link_BETA1-4         : bond        0.00204 (    2)
  link_BETA1-4         : angle       1.74841 (    6)
  hydrogen bonds       : bond        0.04446 (   27)
  hydrogen bonds       : angle       6.09378 (   39)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       3.14124 (    2)
  covalent geometry    : bond        0.00538 ( 1481)
  covalent geometry    : angle       0.68479 ( 2029)

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

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

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  348 Ramachandran restraints generated.
    174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8176 (m110) cc_final: 0.7714 (t0)
REVERT: B  161 MET cc_start: 0.5929 (mmp) cc_final: 0.5409 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1083
  time to fit residues: 4.9567
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 GLU
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0770
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0370
   chunk 9 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0970
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.2414

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.124075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103266 restraints weight = 2301.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107055 restraints weight = 1238.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109544 restraints weight = 803.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   1489  Z= 0.124
  Angle     :  0.657   7.075   2052  Z= 0.313
  Chirality :  0.049   0.215    264
  Planarity :  0.005   0.031    258
  Dihedral  :  6.633  54.528    329
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 23.12 %
    Favored  : 75.62 %
  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: -2.80 (0.66), residues: 174
  helix: -2.74 (0.71), residues: 44
  sheet: -3.01 (1.04), residues: 26
  loop : -1.05 (0.66), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.005   TRP B  62 
 HIS   0.002   0.001   HIS B  64 
 PHE   0.009   0.001   PHE B 147 
 TYR   0.007   0.001   TYR B 103 
 ARG   0.002   0.000   ARG B 149 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00447 (    5)
  link_NAG-ASN         : angle       2.03435 (   15)
  link_BETA1-4         : bond        0.00340 (    2)
  link_BETA1-4         : angle       1.50782 (    6)
  hydrogen bonds       : bond        0.03597 (   27)
  hydrogen bonds       : angle       5.54583 (   39)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       2.43194 (    2)
  covalent geometry    : bond        0.00295 ( 1481)
  covalent geometry    : angle       0.62707 ( 2029)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1192.87 seconds
wall clock time: 21 minutes 46.67 seconds (1306.67 seconds total)