Starting phenix.real_space_refine
on Wed Sep 17 02:59:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w3t_32293/09_2025/7w3t_32293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w3t_32293/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w3t_32293/09_2025/7w3t_32293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w3t_32293/09_2025/7w3t_32293.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w3t_32293/09_2025/7w3t_32293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w3t_32293/09_2025/7w3t_32293.map"
  }
  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-2.0-5805/lib/python3.9/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 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: 0.40, per 1000 atoms: 0.27
  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: 0.18
  Conformation dependent library (CDL) restraints added in 33.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.03
  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: 0.10

  Time building geometry restraints manager: 0.16 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:             0.680
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.220
  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:0.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    3.710
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (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
  covalent geometry    : bond        0.00439 ( 1481)
  covalent geometry    : angle       0.73068 ( 2029)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       3.14491 (    2)
  hydrogen bonds       : bond        0.24601 (   27)
  hydrogen bonds       : angle       7.22475 (   39)
  link_BETA1-4         : bond        0.00303 (    2)
  link_BETA1-4         : angle       1.24640 (    6)
  link_NAG-ASN         : bond        0.00402 (    5)
  link_NAG-ASN         : angle       2.29063 (   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  : 0.029 
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: 0.0261
  time to fit residues: 1.2587
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  : 0.028 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   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**

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 = 0.125117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104444 restraints weight = 2277.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108014 restraints weight = 1281.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110391 restraints weight = 845.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111952 restraints weight = 628.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113120 restraints weight = 506.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1172

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= 0.243
  Angle     :  0.795   9.344   2052  Z= 0.366
  Chirality :  0.054   0.227    264
  Planarity :  0.006   0.034    258
  Dihedral  : 11.221  54.212    329
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.08 (0.62), residues: 174
  helix: -2.89 (0.68), residues: 44
  sheet: -2.85 (0.87), residues: 29
  loop : -1.31 (0.63), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 149 
 TYR   0.015   0.003   TYR B 103 
 PHE   0.014   0.002   PHE B 147 
 TRP   0.027   0.003   TRP B  62 
 HIS   0.004   0.003   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 1481)
  covalent geometry    : angle       0.75312 ( 2029)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       3.70037 (    2)
  hydrogen bonds       : bond        0.05485 (   27)
  hydrogen bonds       : angle       6.64613 (   39)
  link_BETA1-4         : bond        0.00215 (    2)
  link_BETA1-4         : angle       2.64635 (    6)
  link_NAG-ASN         : bond        0.00388 (    5)
  link_NAG-ASN         : angle       2.23756 (   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
  44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8195 (m110) cc_final: 0.7685 (t0)
REVERT: B  127 TYR cc_start: 0.8796 (p90) cc_final: 0.8538 (p90)
REVERT: B  161 MET cc_start: 0.5733 (mmp) cc_final: 0.5362 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 42
  average time/residue: 0.0501
  time to fit residues: 2.4647
Evaluate side-chains
  43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  145 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0970
   chunk 0 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.125848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105151 restraints weight = 2257.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108794 restraints weight = 1253.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111192 restraints weight = 825.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112981 restraints weight = 609.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114171 restraints weight = 485.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   1489  Z= 0.157
  Angle     :  0.685   7.059   2052  Z= 0.321
  Chirality :  0.050   0.220    264
  Planarity :  0.005   0.033    258
  Dihedral  :  7.894  53.453    329
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.58
  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 aren not related in a simple way.
  whole: -3.06 (0.63), residues: 174
  helix: -2.83 (0.69), residues: 44
  sheet: -3.09 (0.93), residues: 27
  loop : -1.30 (0.64), residues: 103

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   0.011   0.002   PHE B 147 
 TRP   0.019   0.002   TRP B  62 
 HIS   0.002   0.002   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 1481)
  covalent geometry    : angle       0.64832 ( 2029)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       2.63256 (    2)
  hydrogen bonds       : bond        0.04411 (   27)
  hydrogen bonds       : angle       5.98113 (   39)
  link_BETA1-4         : bond        0.00265 (    2)
  link_BETA1-4         : angle       2.37810 (    6)
  link_NAG-ASN         : bond        0.00337 (    5)
  link_NAG-ASN         : angle       2.03914 (   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
  45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.060 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8145 (m110) cc_final: 0.7648 (t0)
REVERT: B  127 TYR cc_start: 0.8801 (p90) cc_final: 0.8477 (p90)
REVERT: B  161 MET cc_start: 0.5743 (mmp) cc_final: 0.5235 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 44
  average time/residue: 0.0485
  time to fit residues: 2.5027
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  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   chunk 9 optimal weight:    0.2980
   chunk 7 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.3180

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.125547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104306 restraints weight = 2335.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107936 restraints weight = 1298.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110334 restraints weight = 861.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112069 restraints weight = 643.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113154 restraints weight = 518.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1482

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= 0.153
  Angle     :  0.691   5.681   2052  Z= 0.336
  Chirality :  0.050   0.222    264
  Planarity :  0.005   0.035    258
  Dihedral  :  7.294  53.608    329
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.98 (0.63), residues: 174
  helix: -2.78 (0.70), residues: 44
  sheet: -2.92 (0.95), residues: 27
  loop : -1.26 (0.64), residues: 103

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   0.002   PHE B 147 
 TRP   0.019   0.002   TRP B  62 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 1481)
  covalent geometry    : angle       0.65653 ( 2029)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       3.20893 (    2)
  hydrogen bonds       : bond        0.04105 (   27)
  hydrogen bonds       : angle       6.15432 (   39)
  link_BETA1-4         : bond        0.00110 (    2)
  link_BETA1-4         : angle       2.12296 (    6)
  link_NAG-ASN         : bond        0.00350 (    5)
  link_NAG-ASN         : angle       1.97505 (   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
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8146 (m110) cc_final: 0.7648 (t0)
REVERT: B  127 TYR cc_start: 0.8781 (p90) cc_final: 0.8424 (p90)
REVERT: B  161 MET cc_start: 0.5734 (mmp) cc_final: 0.5154 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0473
  time to fit residues: 2.2532
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  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0570
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.125172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104397 restraints weight = 2257.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107958 restraints weight = 1273.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110422 restraints weight = 842.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112096 restraints weight = 624.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113240 restraints weight = 500.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   1489  Z= 0.166
  Angle     :  0.674   6.045   2052  Z= 0.327
  Chirality :  0.050   0.219    264
  Planarity :  0.005   0.033    258
  Dihedral  :  7.016  53.808    329
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.98 (0.64), residues: 174
  helix: -2.81 (0.70), residues: 44
  sheet: -2.92 (0.96), residues: 27
  loop : -1.25 (0.64), residues: 103

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   0.002   PHE B 147 
 TRP   0.021   0.003   TRP B  62 
 HIS   0.002   0.002   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 1481)
  covalent geometry    : angle       0.64164 ( 2029)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       3.10879 (    2)
  hydrogen bonds       : bond        0.04119 (   27)
  hydrogen bonds       : angle       5.87613 (   39)
  link_BETA1-4         : bond        0.00181 (    2)
  link_BETA1-4         : angle       1.90781 (    6)
  link_NAG-ASN         : bond        0.00318 (    5)
  link_NAG-ASN         : angle       1.90688 (   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
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.067 
Fit side-chains
REVERT: B   41 ASN cc_start: 0.8136 (m110) cc_final: 0.7695 (t0)
REVERT: B  161 MET cc_start: 0.5791 (mmp) cc_final: 0.5218 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0500
  time to fit residues: 2.3257
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  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0570
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 0 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.2898

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.123917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.103170 restraints weight = 2253.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106937 restraints weight = 1222.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109367 restraints weight = 799.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.110986 restraints weight = 591.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112033 restraints weight = 475.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1598

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= 0.139
  Angle     :  0.647   6.210   2052  Z= 0.314
  Chirality :  0.049   0.238    264
  Planarity :  0.005   0.030    258
  Dihedral  :  6.791  54.247    329
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  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 aren not related in a simple way.
  whole: -2.90 (0.64), residues: 174
  helix: -2.70 (0.72), residues: 44
  sheet: -2.88 (0.98), residues: 27
  loop : -1.22 (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
  covalent geometry    : bond        0.00324 ( 1481)
  covalent geometry    : angle       0.61428 ( 2029)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       2.72649 (    2)
  hydrogen bonds       : bond        0.03830 (   27)
  hydrogen bonds       : angle       5.82146 (   39)
  link_BETA1-4         : bond        0.00268 (    2)
  link_BETA1-4         : angle       1.73253 (    6)
  link_NAG-ASN         : bond        0.00415 (    5)
  link_NAG-ASN         : angle       1.98617 (   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  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8146 (m110) cc_final: 0.7647 (t0)
REVERT: B  161 MET cc_start: 0.5799 (mmp) cc_final: 0.5216 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0484
  time to fit residues: 2.3262
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  : 0.056 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0060
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3606 r_free = 0.3606 target = 0.124155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103682 restraints weight = 2211.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107320 restraints weight = 1231.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109725 restraints weight = 808.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.111428 restraints weight = 598.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112422 restraints weight = 482.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1724

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= 0.188
  Angle     :  0.671   6.011   2052  Z= 0.327
  Chirality :  0.050   0.235    264
  Planarity :  0.005   0.031    258
  Dihedral  :  6.828  53.963    329
  Min Nonbonded Distance : 2.565

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.95 (0.64), residues: 174
  helix: -2.79 (0.70), residues: 44
  sheet: -2.86 (1.00), residues: 27
  loop : -1.24 (0.65), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 149 
 TYR   0.011   0.002   TYR B 103 
 PHE   0.012   0.002   PHE B 147 
 TRP   0.028   0.003   TRP B  62 
 HIS   0.003   0.002   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 1481)
  covalent geometry    : angle       0.63849 ( 2029)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       3.04531 (    2)
  hydrogen bonds       : bond        0.04127 (   27)
  hydrogen bonds       : angle       5.91135 (   39)
  link_BETA1-4         : bond        0.00187 (    2)
  link_BETA1-4         : angle       1.74626 (    6)
  link_NAG-ASN         : bond        0.00351 (    5)
  link_NAG-ASN         : angle       2.00309 (   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
  40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8137 (m110) cc_final: 0.7698 (t0)
REVERT: B  161 MET cc_start: 0.5846 (mmp) cc_final: 0.5287 (mmp)
  outliers start: 2
  outliers final: 1
  residues processed: 39
  average time/residue: 0.0546
  time to fit residues: 2.4909
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  : 0.056 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0870
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0070
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.3176

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.125352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.105572 restraints weight = 2155.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109125 restraints weight = 1205.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111514 restraints weight = 797.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113035 restraints weight = 586.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114139 restraints weight = 470.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.1731

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= 0.142
  Angle     :  0.642   5.521   2052  Z= 0.310
  Chirality :  0.049   0.223    264
  Planarity :  0.005   0.030    258
  Dihedral  :  6.694  54.320    329
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 21.25 %
    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 aren not related in a simple way.
  whole: -2.84 (0.65), residues: 174
  helix: -2.66 (0.72), residues: 44
  sheet: -2.81 (1.02), residues: 27
  loop : -1.19 (0.65), 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   0.010   0.002   PHE B 147 
 TRP   0.031   0.004   TRP B  62 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 1481)
  covalent geometry    : angle       0.61035 ( 2029)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       2.57422 (    2)
  hydrogen bonds       : bond        0.03746 (   27)
  hydrogen bonds       : angle       5.72867 (   39)
  link_BETA1-4         : bond        0.00259 (    2)
  link_BETA1-4         : angle       1.59164 (    6)
  link_NAG-ASN         : bond        0.00421 (    5)
  link_NAG-ASN         : angle       2.00420 (   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
  41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.051 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 ASN cc_start: 0.8107 (m110) cc_final: 0.7688 (t0)
REVERT: B  161 MET cc_start: 0.5805 (mmp) cc_final: 0.5239 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0439
  time to fit residues: 2.1351
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  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 2 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0050
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0470
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.1588

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.125248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.104348 restraints weight = 2257.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.108098 restraints weight = 1238.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110488 restraints weight = 812.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112151 restraints weight = 603.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113216 restraints weight = 486.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.1740

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     :  0.618   5.536   2052  Z= 0.301
  Chirality :  0.047   0.213    264
  Planarity :  0.005   0.030    258
  Dihedral  :  6.521  54.146    329
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 21.25 %
    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 aren not related in a simple way.
  whole: -2.65 (0.66), residues: 174
  helix: -2.53 (0.74), residues: 44
  sheet: -2.99 (1.04), residues: 26
  loop : -0.98 (0.65), residues: 104

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   0.006   0.001   PHE B 147 
 TRP   0.035   0.004   TRP B  62 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 1481)
  covalent geometry    : angle       0.58813 ( 2029)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       2.33555 (    2)
  hydrogen bonds       : bond        0.03444 (   27)
  hydrogen bonds       : angle       5.61967 (   39)
  link_BETA1-4         : bond        0.00344 (    2)
  link_BETA1-4         : angle       1.47364 (    6)
  link_NAG-ASN         : bond        0.00475 (    5)
  link_NAG-ASN         : angle       1.96780 (   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: 1
    poor density    : 40
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8443 (m) cc_final: 0.8185 (t)
REVERT: B   41 ASN cc_start: 0.8105 (m110) cc_final: 0.7616 (t0)
REVERT: B  161 MET cc_start: 0.5825 (mmp) cc_final: 0.5279 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.0525
  time to fit residues: 2.4503
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  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 2 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0370
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.2256

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.124512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.103729 restraints weight = 2287.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.107366 restraints weight = 1259.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109824 restraints weight = 833.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.111498 restraints weight = 620.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112512 restraints weight = 498.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   1489  Z= 0.121
  Angle     :  0.615   5.527   2052  Z= 0.300
  Chirality :  0.048   0.214    264
  Planarity :  0.005   0.029    258
  Dihedral  :  6.530  53.971    329
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 21.25 %
    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 aren not related in a simple way.
  whole: -2.68 (0.65), residues: 174
  helix: -2.54 (0.75), residues: 44
  sheet: -3.02 (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   0.007   0.001   TYR B 103 
 PHE   0.007   0.001   PHE B 147 
 TRP   0.052   0.006   TRP B  62 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 1481)
  covalent geometry    : angle       0.58204 ( 2029)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       3.05418 (    2)
  hydrogen bonds       : bond        0.03609 (   27)
  hydrogen bonds       : angle       5.76859 (   39)
  link_BETA1-4         : bond        0.00325 (    2)
  link_BETA1-4         : angle       1.51493 (    6)
  link_NAG-ASN         : bond        0.00447 (    5)
  link_NAG-ASN         : angle       1.94525 (   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
  43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 THR cc_start: 0.8468 (m) cc_final: 0.8207 (t)
REVERT: B   41 ASN cc_start: 0.8121 (m110) cc_final: 0.7638 (t0)
REVERT: B  161 MET cc_start: 0.5825 (mmp) cc_final: 0.5285 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.0483
  time to fit residues: 2.3885
Evaluate side-chains
  42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 17
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 14 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN
B 151 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 = 0.3607 r_free = 0.3607 target = 0.124464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.104202 restraints weight = 2250.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107810 restraints weight = 1246.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110116 restraints weight = 816.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111839 restraints weight = 605.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112884 restraints weight = 483.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   1489  Z= 0.144
  Angle     :  0.638   5.875   2052  Z= 0.310
  Chirality :  0.048   0.215    264
  Planarity :  0.005   0.029    258
  Dihedral  :  6.578  54.017    329
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 21.88 %
    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 aren not related in a simple way.
  whole: -2.62 (0.66), residues: 174
  helix: -2.56 (0.74), residues: 44
  sheet: -2.97 (1.04), residues: 26
  loop : -0.93 (0.65), residues: 104

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   0.043   0.005   TRP B  62 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 1481)
  covalent geometry    : angle       0.60207 ( 2029)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       3.82016 (    2)
  hydrogen bonds       : bond        0.03783 (   27)
  hydrogen bonds       : angle       5.90565 (   39)
  link_BETA1-4         : bond        0.00261 (    2)
  link_BETA1-4         : angle       1.53918 (    6)
  link_NAG-ASN         : bond        0.00414 (    5)
  link_NAG-ASN         : angle       1.95086 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 642.19 seconds
wall clock time: 12 minutes 6.73 seconds (726.73 seconds total)