Starting phenix.real_space_refine
on Wed Jul  1 20:45:29 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_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_32293/07_2026/7w3t_32293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7w3t_32293/07_2026/7w3t_32293.cif"
  }
  resolution = 3.59
  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=   0.012
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 chiralities: 4
  Time building chain proxies: 0.62, per 1000 atoms: 0.43
  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: 0.22
  Conformation dependent library (CDL) restraints added in 52.1 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: 0.05
  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: 0.17

  Time building geometry restraints manager: 0.20 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 -    15.06: 729
       15.06 -    30.12: 83
       30.12 -    45.18: 26
       45.18 -    60.24: 3
       60.24 -    75.30: 2
  Dihedral angle restraints: 843
    sinusoidal: 335
      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=" CA  CYS B  67 "
           pdb=" C   CYS B  67 "
           pdb=" N   ASN B  68 "
           pdb=" CA  ASN B  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.13   17.87     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  GLU B  70 "
           pdb=" C   GLU B  70 "
           pdb=" N   ASN B  71 "
           pdb=" CA  ASN B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.99   17.01     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 840 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:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.600
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
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  : 14.392  75.298    510
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG B 130 
 TYR   0.012   0.002   TYR B 127 
 PHE   0.007   0.001   PHE B 147 
 TRP   0.049   0.006   TRP B  62 
 HIS   0.001   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.21 ( 1481)
  covalent geometry    : angle       0.73068 /  0.34 ( 2029)
  SS BOND              : bond        0.00129 /  0.07 (    1)
  SS BOND              : angle       3.14491 /  1.66 (    2)
  hydrogen bonds       : bond        0.24601 / 18.01 (   27)
  hydrogen bonds       : angle       7.22475 /  5.82 (   39)
  link_BETA1-4         : bond        0.00303 /  0.16 (    2)
  link_BETA1-4         : angle       1.24640 /  0.82 (    6)
  link_NAG-ASN         : bond        0.00402 /  0.20 (    5)
  link_NAG-ASN         : angle       2.29063 /  1.41 (   15)

*********************** 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  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8180 (m110) cc_final: 0.7685 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0480
  time to fit residues: 2.3225
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  : 0.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0670
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0770
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.4276

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.126366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105601 restraints weight = 2275.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.109110 restraints weight = 1279.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111509 restraints weight = 852.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.113049 restraints weight = 635.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114272 restraints weight = 513.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.0965

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= 0.178
  Angle     :  0.713   9.481   2052  Z= 0.333
  Chirality :  0.049   0.206    264
  Planarity :  0.005   0.034    258
  Dihedral  :  4.836  16.941    184
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 14.38 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.62), residues: 174
  helix: -2.77 (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
 ARG   0.003   0.000   ARG B 149 
 TYR   0.012   0.002   TYR B 103 
 PHE   0.012   0.002   PHE B 147 
 TRP   0.025   0.003   TRP B  62 
 HIS   0.003   0.002   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 ( 1481)
  covalent geometry    : angle       0.67797 /  0.32 ( 2029)
  SS BOND              : bond        0.00151 /  0.08 (    1)
  SS BOND              : angle       3.46073 /  1.91 (    2)
  hydrogen bonds       : bond        0.04987 /  3.31 (   27)
  hydrogen bonds       : angle       6.51385 /  5.03 (   39)
  link_BETA1-4         : bond        0.00237 /  0.12 (    2)
  link_BETA1-4         : angle       1.73589 /  1.19 (    6)
  link_NAG-ASN         : bond        0.00341 /  0.17 (    5)
  link_NAG-ASN         : angle       2.12321 /  1.30 (   15)

*********************** 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
  45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8167 (m110) cc_final: 0.7675 (t0)
REVERT: B  127 TYR cc_start: 0.8736 (p90) cc_final: 0.8473 (p90)
REVERT: B  161 MET cc_start: 0.5665 (mmp) cc_final: 0.5289 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0428
  time to fit residues: 2.2256
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  : 0.053 
-------------------------------------------------------------------------------
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 8 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0370
   chunk 3 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    0.0980
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.3458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3644 r_free = 0.3644 target = 0.126316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.105629 restraints weight = 2264.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109187 restraints weight = 1263.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111666 restraints weight = 832.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113311 restraints weight = 615.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114431 restraints weight = 491.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   1489  Z= 0.152
  Angle     :  0.663   6.822   2052  Z= 0.319
  Chirality :  0.048   0.208    264
  Planarity :  0.005   0.033    258
  Dihedral  :  4.788  15.947    184
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.88 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.63), residues: 174
  helix: -2.73 (0.71), residues: 44
  sheet: -2.77 (0.89), residues: 29
  loop : -1.20 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.010   0.002   TYR B 103 
 PHE   0.010   0.001   PHE B 147 
 TRP   0.019   0.002   TRP B  62 
 HIS   0.002   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 1481)
  covalent geometry    : angle       0.63370 /  0.31 ( 2029)
  SS BOND              : bond        0.00094 /  0.05 (    1)
  SS BOND              : angle       2.73803 /  1.51 (    2)
  hydrogen bonds       : bond        0.04411 /  2.92 (   27)
  hydrogen bonds       : angle       6.12385 /  4.79 (   39)
  link_BETA1-4         : bond        0.00132 /  0.07 (    2)
  link_BETA1-4         : angle       1.52030 /  1.02 (    6)
  link_NAG-ASN         : bond        0.00358 /  0.18 (    5)
  link_NAG-ASN         : angle       1.97193 /  1.17 (   15)

*********************** 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
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8177 (m110) cc_final: 0.7675 (t0)
REVERT: B  127 TYR cc_start: 0.8804 (p90) cc_final: 0.8492 (p90)
REVERT: B  161 MET cc_start: 0.5680 (mmp) cc_final: 0.5138 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 42
  average time/residue: 0.0419
  time to fit residues: 2.0837
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0030
   chunk 5 optimal weight:    0.3980
   chunk 11 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0870
   chunk 12 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0980
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.1368

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3661 r_free = 0.3661 target = 0.127811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.107243 restraints weight = 2321.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110781 restraints weight = 1290.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113211 restraints weight = 854.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114881 restraints weight = 632.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115887 restraints weight = 507.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1489  Z= 0.110
  Angle     :  0.629   6.160   2052  Z= 0.309
  Chirality :  0.047   0.202    264
  Planarity :  0.005   0.029    258
  Dihedral  :  4.603  17.131    184
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.64), residues: 174
  helix: -2.57 (0.74), residues: 44
  sheet: -2.89 (0.97), residues: 27
  loop : -1.19 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 149 
 TYR   0.006   0.001   TYR B 103 
 PHE   0.007   0.001   PHE B 197 
 TRP   0.018   0.002   TRP B  62 
 HIS   0.001   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 1481)
  covalent geometry    : angle       0.60449 /  0.30 ( 2029)
  SS BOND              : bond        0.00108 /  0.06 (    1)
  SS BOND              : angle       2.22950 /  1.27 (    2)
  hydrogen bonds       : bond        0.03797 /  2.50 (   27)
  hydrogen bonds       : angle       5.70972 /  4.52 (   39)
  link_BETA1-4         : bond        0.00340 /  0.17 (    2)
  link_BETA1-4         : angle       1.32738 /  0.89 (    6)
  link_NAG-ASN         : bond        0.00412 /  0.20 (    5)
  link_NAG-ASN         : angle       1.83127 /  1.08 (   15)

*********************** 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
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8105 (m110) cc_final: 0.7660 (t0)
REVERT: B  123 SER cc_start: 0.7747 (t) cc_final: 0.7431 (t)
REVERT: B  127 TYR cc_start: 0.8751 (p90) cc_final: 0.8430 (p90)
REVERT: B  161 MET cc_start: 0.5699 (mmp) cc_final: 0.5108 (mmp)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0470
  time to fit residues: 2.2799
Evaluate side-chains
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0050
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.4794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3624 r_free = 0.3624 target = 0.125089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104360 restraints weight = 2248.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107795 restraints weight = 1267.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110287 restraints weight = 845.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111942 restraints weight = 626.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113008 restraints weight = 503.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   1489  Z= 0.197
  Angle     :  0.677   5.884   2052  Z= 0.332
  Chirality :  0.049   0.208    264
  Planarity :  0.005   0.031    258
  Dihedral  :  4.801  15.536    184
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 20.00 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.64), residues: 174
  helix: -2.72 (0.71), residues: 44
  sheet: -2.89 (0.97), residues: 27
  loop : -1.20 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.012   0.002   TYR B 103 
 PHE   0.013   0.002   PHE B 147 
 TRP   0.022   0.003   TRP B  62 
 HIS   0.003   0.002   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.20 ( 1481)
  covalent geometry    : angle       0.64788 /  0.32 ( 2029)
  SS BOND              : bond        0.00145 /  0.08 (    1)
  SS BOND              : angle       3.50124 /  1.99 (    2)
  hydrogen bonds       : bond        0.04376 /  2.87 (   27)
  hydrogen bonds       : angle       5.96625 /  4.73 (   39)
  link_BETA1-4         : bond        0.00102 /  0.05 (    2)
  link_BETA1-4         : angle       1.53470 /  1.06 (    6)
  link_NAG-ASN         : bond        0.00277 /  0.14 (    5)
  link_NAG-ASN         : angle       1.82793 /  1.07 (   15)

*********************** 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
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.053 
Fit side-chains
REVERT: B   41 ASN cc_start: 0.8157 (m110) cc_final: 0.7697 (t0)
REVERT: B  127 TYR cc_start: 0.8800 (p90) cc_final: 0.8420 (p90)
REVERT: B  161 MET cc_start: 0.5778 (mmp) cc_final: 0.5171 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.0463
  time to fit residues: 2.1808
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0170
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 0 optimal weight:    0.3980
   chunk 3 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.3018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3627 r_free = 0.3627 target = 0.125872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105094 restraints weight = 2185.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108725 restraints weight = 1212.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111136 restraints weight = 803.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112739 restraints weight = 600.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113764 restraints weight = 482.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1489  Z= 0.140
  Angle     :  0.640   5.868   2052  Z= 0.312
  Chirality :  0.048   0.233    264
  Planarity :  0.005   0.029    258
  Dihedral  :  4.673  16.460    184
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 20.62 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.83 (0.64), residues: 174
  helix: -2.64 (0.73), residues: 44
  sheet: -2.85 (0.99), residues: 27
  loop : -1.17 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 149 
 TYR   0.009   0.002   TYR B 103 
 PHE   0.009   0.001   PHE B 147 
 TRP   0.021   0.002   TRP B  62 
 HIS   0.002   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 1481)
  covalent geometry    : angle       0.61002 /  0.30 ( 2029)
  SS BOND              : bond        0.00160 /  0.08 (    1)
  SS BOND              : angle       2.88018 /  1.64 (    2)
  hydrogen bonds       : bond        0.03894 /  2.53 (   27)
  hydrogen bonds       : angle       5.73544 /  4.55 (   39)
  link_BETA1-4         : bond        0.00218 /  0.11 (    2)
  link_BETA1-4         : angle       1.38574 /  0.94 (    6)
  link_NAG-ASN         : bond        0.00419 /  0.20 (    5)
  link_NAG-ASN         : angle       1.93334 /  1.13 (   15)

*********************** 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
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.052 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8490 (m) cc_final: 0.8252 (t)
REVERT: B   41 ASN cc_start: 0.8131 (m110) cc_final: 0.7667 (t0)
REVERT: B  161 MET cc_start: 0.5771 (mmp) cc_final: 0.5186 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0432
  time to fit residues: 2.0411
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  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 151 ASN
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.124087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.102790 restraints weight = 2268.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106308 restraints weight = 1260.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108737 restraints weight = 837.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110314 restraints weight = 626.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.111433 restraints weight = 506.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1645

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= 0.201
  Angle     :  0.671   5.773   2052  Z= 0.327
  Chirality :  0.050   0.232    264
  Planarity :  0.005   0.031    258
  Dihedral  :  4.881  15.368    184
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.75 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.64), residues: 174
  helix: -2.83 (0.70), residues: 44
  sheet: -2.87 (1.00), residues: 27
  loop : -1.22 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.012   0.002   TYR B 103 
 PHE   0.013   0.002   PHE B 147 
 TRP   0.030   0.004   TRP B  62 
 HIS   0.003   0.002   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.20 ( 1481)
  covalent geometry    : angle       0.63913 /  0.32 ( 2029)
  SS BOND              : bond        0.00204 /  0.11 (    1)
  SS BOND              : angle       3.42820 /  1.94 (    2)
  hydrogen bonds       : bond        0.04317 /  2.76 (   27)
  hydrogen bonds       : angle       5.94300 /  4.71 (   39)
  link_BETA1-4         : bond        0.00130 /  0.07 (    2)
  link_BETA1-4         : angle       1.51542 /  1.04 (    6)
  link_NAG-ASN         : bond        0.00354 /  0.18 (    5)
  link_NAG-ASN         : angle       1.98047 /  1.16 (   15)

*********************** 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
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8164 (m110) cc_final: 0.7705 (t0)
REVERT: B  161 MET cc_start: 0.5873 (mmp) cc_final: 0.5297 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0397
  time to fit residues: 1.9253
Evaluate side-chains
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0980
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0270
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.3038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3602 r_free = 0.3602 target = 0.123751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102986 restraints weight = 2223.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106685 restraints weight = 1235.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109143 restraints weight = 806.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.110655 restraints weight = 595.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111691 restraints weight = 478.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1489  Z= 0.139
  Angle     :  0.660   6.725   2052  Z= 0.313
  Chirality :  0.048   0.219    264
  Planarity :  0.005   0.029    258
  Dihedral  :  4.753  15.595    184
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 20.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.64), residues: 174
  helix: -2.70 (0.72), residues: 44
  sheet: -2.85 (1.01), residues: 27
  loop : -1.15 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.009   0.002   TYR B 103 
 PHE   0.010   0.002   PHE B 147 
 TRP   0.030   0.004   TRP B  62 
 HIS   0.002   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 1481)
  covalent geometry    : angle       0.63070 /  0.31 ( 2029)
  SS BOND              : bond        0.00182 /  0.10 (    1)
  SS BOND              : angle       2.86567 /  1.63 (    2)
  hydrogen bonds       : bond        0.03901 /  2.52 (   27)
  hydrogen bonds       : angle       5.70253 /  4.55 (   39)
  link_BETA1-4         : bond        0.00203 /  0.11 (    2)
  link_BETA1-4         : angle       1.37013 /  0.93 (    6)
  link_NAG-ASN         : bond        0.00407 /  0.20 (    5)
  link_NAG-ASN         : angle       1.98622 /  1.15 (   15)

*********************** 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
  39 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8143 (m110) cc_final: 0.7667 (t0)
REVERT: B  161 MET cc_start: 0.5837 (mmp) cc_final: 0.5247 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 37
  average time/residue: 0.0527
  time to fit residues: 2.2506
Evaluate side-chains
  39 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
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 16 optimal weight:    0.0050
   chunk 2 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 0 optimal weight:    0.0980
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.1772

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3614 r_free = 0.3614 target = 0.125074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.104219 restraints weight = 2251.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107816 restraints weight = 1236.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.110257 restraints weight = 815.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.111867 restraints weight = 605.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113031 restraints weight = 486.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   1489  Z= 0.109
  Angle     :  0.624   6.293   2052  Z= 0.297
  Chirality :  0.047   0.211    264
  Planarity :  0.004   0.029    258
  Dihedral  :  4.480  14.782    184
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 20.62 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.67 (0.65), residues: 174
  helix: -2.54 (0.74), residues: 44
  sheet: -2.76 (1.04), residues: 27
  loop : -1.05 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 149 
 TYR   0.006   0.001   TYR B 103 
 PHE   0.007   0.001   PHE B 147 
 TRP   0.036   0.004   TRP B  62 
 HIS   0.002   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 ( 1481)
  covalent geometry    : angle       0.59554 /  0.29 ( 2029)
  SS BOND              : bond        0.00148 /  0.08 (    1)
  SS BOND              : angle       2.41466 /  1.38 (    2)
  hydrogen bonds       : bond        0.03462 /  2.26 (   27)
  hydrogen bonds       : angle       5.47180 /  4.44 (   39)
  link_BETA1-4         : bond        0.00333 /  0.17 (    2)
  link_BETA1-4         : angle       1.29604 /  0.90 (    6)
  link_NAG-ASN         : bond        0.00453 /  0.22 (    5)
  link_NAG-ASN         : angle       1.94177 /  1.12 (   15)

*********************** 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  : 0.048 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8456 (m) cc_final: 0.8200 (t)
REVERT: B   41 ASN cc_start: 0.8118 (m110) cc_final: 0.7629 (t0)
REVERT: B  123 SER cc_start: 0.7789 (t) cc_final: 0.7468 (t)
REVERT: B  161 MET cc_start: 0.5797 (mmp) cc_final: 0.5205 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.0326
  time to fit residues: 1.5132
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  : 0.050 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 14 optimal weight:    0.3980
   chunk 13 optimal weight:    0.1980
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 7 optimal weight:    0.0370
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.1394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3624 r_free = 0.3624 target = 0.125714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.105078 restraints weight = 2266.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108714 restraints weight = 1235.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111154 restraints weight = 812.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112750 restraints weight = 601.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.113735 restraints weight = 482.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   1489  Z= 0.102
  Angle     :  0.608   6.200   2052  Z= 0.289
  Chirality :  0.047   0.208    264
  Planarity :  0.004   0.029    258
  Dihedral  :  4.536  18.986    184
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.65), residues: 174
  helix: -2.49 (0.76), residues: 44
  sheet: -2.68 (1.04), residues: 27
  loop : -0.97 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 130 
 TYR   0.005   0.001   TYR B 103 
 PHE   0.006   0.001   PHE B 147 
 TRP   0.035   0.004   TRP B  62 
 HIS   0.001   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.10 ( 1481)
  covalent geometry    : angle       0.58114 /  0.28 ( 2029)
  SS BOND              : bond        0.00205 /  0.11 (    1)
  SS BOND              : angle       2.11070 /  1.21 (    2)
  hydrogen bonds       : bond        0.03308 /  2.15 (   27)
  hydrogen bonds       : angle       5.46741 /  4.49 (   39)
  link_BETA1-4         : bond        0.00369 /  0.19 (    2)
  link_BETA1-4         : angle       1.29316 /  0.92 (    6)
  link_NAG-ASN         : bond        0.00467 /  0.23 (    5)
  link_NAG-ASN         : angle       1.90323 /  1.10 (   15)

********************** 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
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8456 (m) cc_final: 0.8198 (t)
REVERT: B   41 ASN cc_start: 0.8110 (m110) cc_final: 0.7626 (t0)
REVERT: B  123 SER cc_start: 0.7803 (t) cc_final: 0.7500 (t)
REVERT: B  161 MET cc_start: 0.5826 (mmp) cc_final: 0.5270 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 40
  average time/residue: 0.0434
  time to fit residues: 2.0488
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  : 0.050 
-------------------------------------------------------------------------------
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 7 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  58 ASN
B  71 ASN
** B 153 ASN ** 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 = 0.3589 r_free = 0.3589 target = 0.122608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.101626 restraints weight = 2278.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105251 restraints weight = 1258.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107625 restraints weight = 833.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.109164 restraints weight = 614.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110315 restraints weight = 495.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   1489  Z= 0.207
  Angle     :  0.696   6.044   2052  Z= 0.334
  Chirality :  0.050   0.220    264
  Planarity :  0.005   0.033    258
  Dihedral  :  4.984  19.758    184
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.65), residues: 174
  helix: -2.78 (0.71), residues: 44
  sheet: -3.06 (1.02), residues: 26
  loop : -1.00 (0.65), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 149 
 TYR   0.012   0.002   TYR B 103 
 PHE   0.013   0.002   PHE B 147 
 TRP   0.046   0.006   TRP B  62 
 HIS   0.003   0.002   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.21 ( 1481)
  covalent geometry    : angle       0.66569 /  0.33 ( 2029)
  SS BOND              : bond        0.00225 /  0.12 (    1)
  SS BOND              : angle       3.35039 /  1.89 (    2)
  hydrogen bonds       : bond        0.04055 /  2.57 (   27)
  hydrogen bonds       : angle       5.86117 /  4.60 (   39)
  link_BETA1-4         : bond        0.00198 /  0.10 (    2)
  link_BETA1-4         : angle       1.54587 /  1.10 (    6)
  link_NAG-ASN         : bond        0.00320 /  0.16 (    5)
  link_NAG-ASN         : angle       1.94910 /  1.15 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 644.16 seconds
wall clock time: 11 minutes 55.83 seconds (715.83 seconds total)