Starting phenix.real_space_refine
on Fri Aug 22 13:52:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr0_34041/08_2025/7yr0_34041.cif"
  }
  resolution = 3.98
  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=  -0.001 sd=   0.044
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      15      5.16       5
     C    2149      2.51       5
     N     571      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3383
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1560
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "C"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 959
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 815
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.11, per 1000 atoms: 0.33
  Number of scatterers: 3383
  At special positions: 0
  Unit cell: (73.83, 85.6, 81.32, 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      15     16.00
     O     648      8.00
     N     571      7.00
     C    2149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " 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 D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG D   1 " - " FUC D   4 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 133.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      6.3% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.995A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 342'
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.799A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'C' and resid 61 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.310A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.597A  pdb=" N   TYR A 453 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASN C 116 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.890A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.697A  pdb=" N   LEU B  11 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22
      removed outlier: 3.763A  pdb=" N   ASP B  71 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47
      removed outlier: 4.117A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    189 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: 0.30

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1073
        1.35 -     1.46: 942
        1.46 -     1.58: 1439
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3472
  Sorted by residual:
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C2  NAG D   2 "
       pdb=" N2  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" CA  GLY A 381 "
       pdb=" C   GLY A 381 "
    ideal  model  delta    sigma   weight residual
    1.512  1.523 -0.011 8.70e-03 1.32e+04 1.56e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.36e+00
  ... (remaining 3467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 4462
        1.26 -     2.51: 185
        2.51 -     3.77: 51
        3.77 -     5.02: 17
        5.02 -     6.28: 5
  Bond angle restraints: 4720
  Sorted by residual:
  angle pdb=" N   ILE A 402 "
        pdb=" CA  ILE A 402 "
        pdb=" C   ILE A 402 "
      ideal   model   delta    sigma   weight residual
     108.53  111.81   -3.28 1.22e+00 6.72e-01 7.23e+00
  angle pdb=" C   GLU C  82 "
        pdb=" CA  GLU C  82 "
        pdb=" CB  GLU C  82 "
      ideal   model   delta    sigma   weight residual
     110.42  115.40   -4.98 1.99e+00 2.53e-01 6.25e+00
  angle pdb=" C   GLU B  80 "
        pdb=" CA  GLU B  80 "
        pdb=" CB  GLU B  80 "
      ideal   model   delta    sigma   weight residual
     109.26  112.83   -3.57 1.47e+00 4.63e-01 5.91e+00
  angle pdb=" C   MET C  48 "
        pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
      ideal   model   delta    sigma   weight residual
     121.46  119.21    2.25 9.50e-01 1.11e+00 5.63e+00
  angle pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
        pdb=" C   GLY C  49 "
      ideal   model   delta    sigma   weight residual
     110.90  114.36   -3.46 1.53e+00 4.27e-01 5.12e+00
  ... (remaining 4715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.07: 1915
       22.07 -    44.14: 136
       44.14 -    66.21: 11
       66.21 -    88.28: 9
       88.28 -   110.35: 5
  Dihedral angle restraints: 2076
    sinusoidal: 851
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CA  SER B   7 "
           pdb=" C   SER B   7 "
           pdb=" N   PRO B   8 "
           pdb=" CA  PRO B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.67   38.33     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  TYR C  80 "
           pdb=" C   TYR C  80 "
           pdb=" N   MET C  81 "
           pdb=" CA  MET C  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 448
       0.066 -    0.133: 61
       0.133 -    0.199: 4
       0.199 -    0.265: 0
       0.265 -    0.331: 2
  Chirality restraints: 515
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 512 not shown)

  Planarity restraints: 606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B   7 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO B   8 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B   8 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B   8 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C  47 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TRP C  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET C  48 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  47 "    0.009 2.00e-02 2.50e+03   7.14e-03 1.27e+00
        pdb=" CG  TRP C  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  47 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  47 "    0.001 2.00e-02 2.50e+03
  ... (remaining 603 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 130
        2.71 -     3.26: 3238
        3.26 -     3.81: 5061
        3.81 -     4.35: 6100
        4.35 -     4.90: 10380
  Nonbonded interactions: 24909
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  69 "
            pdb=" OE2 GLU C  82 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   VAL B   3 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C  35 "
            pdb=" OD2 ASP C  99 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" NH1 ARG C  87 "
            pdb=" OD1 ASP C  89 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   ALA A 419 "
            pdb=" NZ  LYS A 424 "
     model   vdw
     2.259 3.120
  ... (remaining 24904 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:             4.290
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.250
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
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      :  0.003   0.028   3481  Z= 0.154
  Angle     :  0.708   8.519   4742  Z= 0.353
  Chirality :  0.049   0.331    515
  Planarity :  0.004   0.034    605
  Dihedral  : 15.968 110.350   1287
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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: -1.76 (0.43), residues: 421
  helix: -0.21 (3.10), residues: 6
  sheet:  0.50 (0.59), residues: 92
  loop : -1.86 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.012   0.001   TYR B  50 
 PHE   0.017   0.001   PHE C  29 
 TRP   0.020   0.001   TRP C  47 
 HIS   0.002   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3472)
  covalent geometry    : angle       0.68081 ( 4720)
  SS BOND              : bond        0.00316 (    5)
  SS BOND              : angle       0.74826 (   10)
  hydrogen bonds       : bond        0.13084 (   71)
  hydrogen bonds       : angle       5.73812 (  189)
  link_BETA1-4         : bond        0.00448 (    2)
  link_BETA1-4         : angle       2.64261 (    6)
  link_BETA1-6         : bond        0.00327 (    1)
  link_BETA1-6         : angle       1.33975 (    3)
  link_NAG-ASN         : bond        0.02652 (    1)
  link_NAG-ASN         : angle       6.73296 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.124 
Fit side-chains
REVERT: C   80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7822 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0691
  time to fit residues: 6.2548
Evaluate side-chains
  57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0670
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.124755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098438 restraints weight = 8098.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100949 restraints weight = 5453.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.102738 restraints weight = 4244.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.103969 restraints weight = 3583.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.104430 restraints weight = 3189.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3481  Z= 0.138
  Angle     :  0.690   9.550   4742  Z= 0.330
  Chirality :  0.046   0.257    515
  Planarity :  0.004   0.037    605
  Dihedral  :  9.988  67.700    552
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.92 %
    Favored  : 85.67 %
  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: -1.86 (0.42), residues: 421
  helix: -2.03 (1.64), residues: 12
  sheet:  0.28 (0.58), residues: 98
  loop : -1.87 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  38 
 TYR   0.024   0.002   TYR B  50 
 PHE   0.012   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3472)
  covalent geometry    : angle       0.65519 ( 4720)
  SS BOND              : bond        0.00366 (    5)
  SS BOND              : angle       0.69234 (   10)
  hydrogen bonds       : bond        0.03300 (   71)
  hydrogen bonds       : angle       5.56304 (  189)
  link_BETA1-4         : bond        0.00357 (    2)
  link_BETA1-4         : angle       2.62481 (    6)
  link_BETA1-6         : bond        0.00543 (    1)
  link_BETA1-6         : angle       1.04478 (    3)
  link_NAG-ASN         : bond        0.02210 (    1)
  link_NAG-ASN         : angle       7.75018 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0793
  time to fit residues: 6.4208
Evaluate side-chains
  59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.125069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.098468 restraints weight = 7951.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.101142 restraints weight = 5217.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.102964 restraints weight = 4002.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.103739 restraints weight = 3364.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.104909 restraints weight = 3063.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3481  Z= 0.122
  Angle     :  0.679   9.560   4742  Z= 0.318
  Chirality :  0.046   0.269    515
  Planarity :  0.004   0.034    605
  Dihedral  :  7.873  59.472    552
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.60 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.61 %
    Favored  : 83.71 %
  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: -1.78 (0.42), residues: 421
  helix: -1.93 (1.71), residues: 12
  sheet:  0.64 (0.59), residues: 92
  loop : -1.88 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 346 
 TYR   0.012   0.001   TYR A 501 
 PHE   0.017   0.001   PHE C  29 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3472)
  covalent geometry    : angle       0.64350 ( 4720)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       0.75453 (   10)
  hydrogen bonds       : bond        0.02965 (   71)
  hydrogen bonds       : angle       5.41904 (  189)
  link_BETA1-4         : bond        0.00567 (    2)
  link_BETA1-4         : angle       2.68369 (    6)
  link_BETA1-6         : bond        0.00360 (    1)
  link_BETA1-6         : angle       0.97001 (    3)
  link_NAG-ASN         : bond        0.02300 (    1)
  link_NAG-ASN         : angle       7.73392 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.153 
Fit side-chains
REVERT: C   80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7713 (m-80)
REVERT: C   82 GLU cc_start: 0.6034 (pp20) cc_final: 0.5489 (tm-30)
REVERT: C   87 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7818 (tmm-80)
  outliers start: 6
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0767
  time to fit residues: 6.1939
Evaluate side-chains
  62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.124386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.098492 restraints weight = 7922.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100941 restraints weight = 5356.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.102707 restraints weight = 4189.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.103882 restraints weight = 3546.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104350 restraints weight = 3170.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3481  Z= 0.140
  Angle     :  0.671   9.497   4742  Z= 0.321
  Chirality :  0.047   0.252    515
  Planarity :  0.004   0.035    605
  Dihedral  :  7.049  58.579    552
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.08 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.26 %
    Favored  : 79.49 %
  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: -1.74 (0.42), residues: 421
  helix: -1.71 (1.81), residues: 12
  sheet:  0.41 (0.59), residues: 98
  loop : -1.81 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  87 
 TYR   0.021   0.001   TYR B  50 
 PHE   0.015   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3472)
  covalent geometry    : angle       0.63700 ( 4720)
  SS BOND              : bond        0.00349 (    5)
  SS BOND              : angle       0.80418 (   10)
  hydrogen bonds       : bond        0.02956 (   71)
  hydrogen bonds       : angle       5.50847 (  189)
  link_BETA1-4         : bond        0.00394 (    2)
  link_BETA1-4         : angle       2.49991 (    6)
  link_BETA1-6         : bond        0.00311 (    1)
  link_BETA1-6         : angle       1.08369 (    3)
  link_NAG-ASN         : bond        0.02380 (    1)
  link_NAG-ASN         : angle       7.51363 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.8051 (m-80) cc_final: 0.7795 (m-80)
REVERT: C   82 GLU cc_start: 0.5787 (pp20) cc_final: 0.5307 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0683
  time to fit residues: 5.6339
Evaluate side-chains
  61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0870
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.3362

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.122218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096005 restraints weight = 8112.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098450 restraints weight = 5484.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100079 restraints weight = 4290.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.101243 restraints weight = 3660.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101931 restraints weight = 3279.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3481  Z= 0.187
  Angle     :  0.716   9.729   4742  Z= 0.345
  Chirality :  0.047   0.246    515
  Planarity :  0.004   0.033    605
  Dihedral  :  7.076  58.849    552
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.74 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.22 %
    Favored  : 76.97 %
  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: -1.90 (0.41), residues: 421
  helix: -1.93 (1.26), residues: 20
  sheet:  0.36 (0.58), residues: 97
  loop : -1.92 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  87 
 TYR   0.023   0.002   TYR B  50 
 PHE   0.010   0.002   PHE A 342 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.016   0.003   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3472)
  covalent geometry    : angle       0.68607 ( 4720)
  SS BOND              : bond        0.00445 (    5)
  SS BOND              : angle       0.87393 (   10)
  hydrogen bonds       : bond        0.03184 (   71)
  hydrogen bonds       : angle       5.67993 (  189)
  link_BETA1-4         : bond        0.00336 (    2)
  link_BETA1-4         : angle       2.46644 (    6)
  link_BETA1-6         : bond        0.00068 (    1)
  link_BETA1-6         : angle       1.06093 (    3)
  link_NAG-ASN         : bond        0.02738 (    1)
  link_NAG-ASN         : angle       7.29054 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5865 (pp20) cc_final: 0.5459 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0657
  time to fit residues: 5.2575
Evaluate side-chains
  61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0970
   overall best weight:    0.5900

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.124310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.098277 restraints weight = 8119.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.100720 restraints weight = 5474.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.102458 restraints weight = 4275.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103315 restraints weight = 3631.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104429 restraints weight = 3289.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3481  Z= 0.123
  Angle     :  0.689   9.565   4742  Z= 0.329
  Chirality :  0.048   0.296    515
  Planarity :  0.003   0.035    605
  Dihedral  :  6.767  57.253    552
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.08 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 18.82 %
    Favored  : 76.69 %
  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: -1.65 (0.42), residues: 421
  helix: -1.74 (1.78), residues: 12
  sheet:  0.62 (0.59), residues: 92
  loop : -1.75 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.022   0.001   TYR B  50 
 PHE   0.007   0.001   PHE A 374 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3472)
  covalent geometry    : angle       0.65611 ( 4720)
  SS BOND              : bond        0.00352 (    5)
  SS BOND              : angle       0.88286 (   10)
  hydrogen bonds       : bond        0.02817 (   71)
  hydrogen bonds       : angle       5.54973 (  189)
  link_BETA1-4         : bond        0.00616 (    2)
  link_BETA1-4         : angle       3.45413 (    6)
  link_BETA1-6         : bond        0.00212 (    1)
  link_BETA1-6         : angle       1.27930 (    3)
  link_NAG-ASN         : bond        0.02828 (    1)
  link_NAG-ASN         : angle       6.65140 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5336 (tm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0647
  time to fit residues: 5.5025
Evaluate side-chains
  64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.123781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098978 restraints weight = 7949.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.101310 restraints weight = 5374.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.102910 restraints weight = 4179.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.104156 restraints weight = 3544.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.104995 restraints weight = 3144.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3481  Z= 0.154
  Angle     :  0.695   9.525   4742  Z= 0.339
  Chirality :  0.048   0.266    515
  Planarity :  0.003   0.033    605
  Dihedral  :  6.654  57.943    552
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.26 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.66 %
    Favored  : 76.97 %
  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: -1.79 (0.41), residues: 421
  helix: -2.09 (1.22), residues: 20
  sheet:  0.69 (0.59), residues: 90
  loop : -1.86 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.020   0.001   TYR B  50 
 PHE   0.009   0.001   PHE A 400 
 TRP   0.008   0.001   TRP C  47 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3472)
  covalent geometry    : angle       0.67108 ( 4720)
  SS BOND              : bond        0.00389 (    5)
  SS BOND              : angle       0.90401 (   10)
  hydrogen bonds       : bond        0.02938 (   71)
  hydrogen bonds       : angle       5.58156 (  189)
  link_BETA1-4         : bond        0.00728 (    2)
  link_BETA1-4         : angle       3.10756 (    6)
  link_BETA1-6         : bond        0.00222 (    1)
  link_BETA1-6         : angle       1.42515 (    3)
  link_NAG-ASN         : bond        0.03312 (    1)
  link_NAG-ASN         : angle       5.49876 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5412 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 67
  average time/residue: 0.0734
  time to fit residues: 5.9470
Evaluate side-chains
  68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0670
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.125426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.100435 restraints weight = 7925.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.103047 restraints weight = 5181.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104628 restraints weight = 3941.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106134 restraints weight = 3316.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106951 restraints weight = 2908.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3481  Z= 0.121
  Angle     :  0.685   9.542   4742  Z= 0.329
  Chirality :  0.046   0.251    515
  Planarity :  0.003   0.034    605
  Dihedral  :  6.435  58.160    552
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.84 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.22 %
    Favored  : 76.40 %
  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: -1.68 (0.42), residues: 421
  helix: -1.85 (1.72), residues: 12
  sheet:  0.52 (0.58), residues: 95
  loop : -1.77 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.020   0.001   TYR B  50 
 PHE   0.006   0.001   PHE A 377 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.020   0.004   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3472)
  covalent geometry    : angle       0.66044 ( 4720)
  SS BOND              : bond        0.00323 (    5)
  SS BOND              : angle       0.88439 (   10)
  hydrogen bonds       : bond        0.02765 (   71)
  hydrogen bonds       : angle       5.43533 (  189)
  link_BETA1-4         : bond        0.00599 (    2)
  link_BETA1-4         : angle       3.20221 (    6)
  link_BETA1-6         : bond        0.00248 (    1)
  link_BETA1-6         : angle       1.18631 (    3)
  link_NAG-ASN         : bond        0.02891 (    1)
  link_NAG-ASN         : angle       5.64716 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5434 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0659
  time to fit residues: 5.3975
Evaluate side-chains
  68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.2980
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0000
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.126118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101702 restraints weight = 7907.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.104221 restraints weight = 5271.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105979 restraints weight = 4046.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107040 restraints weight = 3393.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.107311 restraints weight = 3024.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3481  Z= 0.112
  Angle     :  0.665   9.624   4742  Z= 0.319
  Chirality :  0.045   0.248    515
  Planarity :  0.003   0.033    605
  Dihedral  :  6.228  58.489    552
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.08 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 19.94 %
    Favored  : 76.97 %
  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: -1.65 (0.42), residues: 421
  helix: -1.88 (1.70), residues: 12
  sheet:  0.52 (0.59), residues: 95
  loop : -1.74 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.019   0.001   TYR B  50 
 PHE   0.006   0.001   PHE A 377 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3472)
  covalent geometry    : angle       0.63900 ( 4720)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       0.86479 (   10)
  hydrogen bonds       : bond        0.02838 (   71)
  hydrogen bonds       : angle       5.36465 (  189)
  link_BETA1-4         : bond        0.00528 (    2)
  link_BETA1-4         : angle       2.94132 (    6)
  link_BETA1-6         : bond        0.00359 (    1)
  link_BETA1-6         : angle       1.21778 (    3)
  link_NAG-ASN         : bond        0.02723 (    1)
  link_NAG-ASN         : angle       5.89217 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5877 (OUTLIER) cc_final: 0.5541 (tm-30)
REVERT: C   94 TYR cc_start: 0.7860 (m-80) cc_final: 0.7507 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0607
  time to fit residues: 4.9930
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.125254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099869 restraints weight = 8015.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102421 restraints weight = 5304.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.104212 restraints weight = 4071.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105261 restraints weight = 3412.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105260 restraints weight = 3049.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3481  Z= 0.132
  Angle     :  0.692   9.639   4742  Z= 0.334
  Chirality :  0.045   0.240    515
  Planarity :  0.003   0.034    605
  Dihedral  :  6.349  58.975    552
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.07 %
    Favored  : 76.40 %
  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: -1.63 (0.42), residues: 421
  helix: -1.81 (1.73), residues: 12
  sheet:  0.60 (0.59), residues: 93
  loop : -1.73 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.019   0.001   TYR B  50 
 PHE   0.020   0.001   PHE A 429 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3472)
  covalent geometry    : angle       0.66913 ( 4720)
  SS BOND              : bond        0.00347 (    5)
  SS BOND              : angle       0.84944 (   10)
  hydrogen bonds       : bond        0.02843 (   71)
  hydrogen bonds       : angle       5.44807 (  189)
  link_BETA1-4         : bond        0.00403 (    2)
  link_BETA1-4         : angle       2.64873 (    6)
  link_BETA1-6         : bond        0.00330 (    1)
  link_BETA1-6         : angle       1.24505 (    3)
  link_NAG-ASN         : bond        0.02766 (    1)
  link_NAG-ASN         : angle       5.84837 (    3)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5599 (tm-30)
  outliers start: 9
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0709
  time to fit residues: 5.5217
Evaluate side-chains
  65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain C residue   82 GLU
Chi-restraints excluded: chain B residue   82 GLU
Chi-restraints excluded: chain B residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.125519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.099981 restraints weight = 8088.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102490 restraints weight = 5322.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104315 restraints weight = 4085.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.105575 restraints weight = 3419.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.106062 restraints weight = 3025.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3481  Z= 0.132
  Angle     :  0.692   9.652   4742  Z= 0.335
  Chirality :  0.046   0.241    515
  Planarity :  0.003   0.033    605
  Dihedral  :  6.350  59.109    552
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.63 %
    Favored  : 75.84 %
  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: -1.63 (0.42), residues: 421
  helix: -1.82 (1.71), residues: 12
  sheet:  0.60 (0.59), residues: 93
  loop : -1.73 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.019   0.001   TYR B  50 
 PHE   0.020   0.001   PHE A 429 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3472)
  covalent geometry    : angle       0.66970 ( 4720)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       0.86935 (   10)
  hydrogen bonds       : bond        0.02849 (   71)
  hydrogen bonds       : angle       5.45618 (  189)
  link_BETA1-4         : bond        0.00395 (    2)
  link_BETA1-4         : angle       2.57225 (    6)
  link_BETA1-6         : bond        0.00272 (    1)
  link_BETA1-6         : angle       1.23336 (    3)
  link_NAG-ASN         : bond        0.02660 (    1)
  link_NAG-ASN         : angle       5.89589 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 788.93 seconds
wall clock time: 14 minutes 20.92 seconds (860.92 seconds total)