Starting phenix.real_space_refine
on Tue Mar  3 11:34:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2026/7wt9_32772.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2117      2.51       5
     N     564      2.21       5
     O     646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3343
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 900
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "A"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 831
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100}
  Time building chain proxies: 0.80, per 1000 atoms: 0.24
  Number of scatterers: 3343
  At special positions: 0
  Unit cell: (63.44, 80.08, 105.04, 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      16     16.00
     O     646      8.00
     N     564      7.00
     C    2117      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " 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
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 138.0 milliseconds
  

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      10.0% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.734A  pdb=" N   LYS H  64 " --> pdb=" O   ASP H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 372
      removed outlier: 3.525A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA E 372 " --> pdb=" O   LEU E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
      removed outlier: 3.716A  pdb=" N   LEU E 387 " --> pdb=" O   PRO E 384 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 410
    Processing helix  chain 'E' and resid 417 through 422
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 4.116A  pdb=" N   ILE A  83 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.562A  pdb=" N   SER H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 5.790A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 395 through 397
    Processing sheet with id=AA4, first strand: chain 'E' and resid 400 through 402
      removed outlier: 3.579A  pdb=" N   PHE E 400 " --> pdb=" O   VAL E 510 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'A' and resid 22 through 24
      removed outlier: 3.510A  pdb=" N   THR A  72 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR A  74 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   SER A  63 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.515A  pdb=" N   GLN A  38 " --> pdb=" O   THR A  85 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR A  85 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   THR A  97 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)

    58 hydrogen bonds defined for protein.
    156 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: 0.33

  Time building geometry restraints manager: 0.29 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: 1078
        1.35 -     1.47: 865
        1.47 -     1.59: 1460
        1.59 -     1.70: 0
        1.70 -     1.82: 20
  Bond restraints: 3423
  Sorted by residual:
  bond pdb=" N   VAL E 445 "
       pdb=" CA  VAL E 445 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.07e+00
  bond pdb=" N   LYS E 444 "
       pdb=" CA  LYS E 444 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.23e-02 6.61e+03 7.60e+00
  bond pdb=" C   SER A   7 "
       pdb=" N   PRO A   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.33e+00
  bond pdb=" N   SER E 446 "
       pdb=" CA  SER E 446 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.19e+00
  bond pdb=" N   ASN E 448 "
       pdb=" CA  ASN E 448 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.027 1.28e-02 6.10e+03 4.37e+00
  ... (remaining 3418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 4495
        3.18 -     6.36: 137
        6.36 -     9.54: 18
        9.54 -    12.72: 3
       12.72 -    15.90: 1
  Bond angle restraints: 4654
  Sorted by residual:
  angle pdb=" C   GLY A  68 "
        pdb=" N   THR A  69 "
        pdb=" CA  THR A  69 "
      ideal   model   delta    sigma   weight residual
     123.91  131.91   -8.00 1.66e+00 3.63e-01 2.32e+01
  angle pdb=" CA  GLN E 409 "
        pdb=" CB  GLN E 409 "
        pdb=" CG  GLN E 409 "
      ideal   model   delta    sigma   weight residual
     114.10  123.38   -9.28 2.00e+00 2.50e-01 2.15e+01
  angle pdb=" CA  LEU E 518 "
        pdb=" CB  LEU E 518 "
        pdb=" CG  LEU E 518 "
      ideal   model   delta    sigma   weight residual
     116.30  132.20  -15.90 3.50e+00 8.16e-02 2.06e+01
  angle pdb=" CB  MET A   4 "
        pdb=" CG  MET A   4 "
        pdb=" SD  MET A   4 "
      ideal   model   delta    sigma   weight residual
     112.70  124.79  -12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" CB  GLU E 340 "
        pdb=" CG  GLU E 340 "
        pdb=" CD  GLU E 340 "
      ideal   model   delta    sigma   weight residual
     112.60  119.08   -6.48 1.70e+00 3.46e-01 1.46e+01
  ... (remaining 4649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 1826
       17.01 -    34.02: 162
       34.02 -    51.04: 38
       51.04 -    68.05: 4
       68.05 -    85.06: 4
  Dihedral angle restraints: 2034
    sinusoidal: 787
      harmonic: 1247
  Sorted by residual:
  dihedral pdb=" CB  CYS E 336 "
           pdb=" SG  CYS E 336 "
           pdb=" SG  CYS E 361 "
           pdb=" CB  CYS E 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.66  -82.66     1      1.00e+01 1.00e-02 8.37e+01
  dihedral pdb=" CB  CYS E 379 "
           pdb=" SG  CYS E 379 "
           pdb=" SG  CYS E 432 "
           pdb=" CB  CYS E 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -13.69  -72.31     1      1.00e+01 1.00e-02 6.68e+01
  dihedral pdb=" CA  GLU H  98 "
           pdb=" C   GLU H  98 "
           pdb=" N   VAL H  99 "
           pdb=" CA  VAL H  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.14  -37.86     0      5.00e+00 4.00e-02 5.73e+01
  ... (remaining 2031 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 442
       0.100 -    0.200: 58
       0.200 -    0.300: 4
       0.300 -    0.400: 1
       0.400 -    0.500: 2
  Chirality restraints: 507
  Sorted by residual:
  chirality pdb=" CB  THR H 114 "
            pdb=" CA  THR H 114 "
            pdb=" OG1 THR H 114 "
            pdb=" CG2 THR H 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.05    0.50 2.00e-01 2.50e+01 6.24e+00
  chirality pdb=" CB  ILE E 402 "
            pdb=" CA  ILE E 402 "
            pdb=" CG1 ILE E 402 "
            pdb=" CG2 ILE E 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.26e+00
  chirality pdb=" CB  VAL E 341 "
            pdb=" CA  VAL E 341 "
            pdb=" CG1 VAL E 341 "
            pdb=" CG2 VAL E 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 504 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  35 "   -0.015 2.00e-02 2.50e+03   2.46e-02 1.52e+01
        pdb=" CG  TRP A  35 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  35 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  35 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  35 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  35 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  35 "   -0.019 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  35 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  50 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.16e+00
        pdb=" C   ASP A  50 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ASP A  50 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A  51 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 351 "    0.014 2.00e-02 2.50e+03   1.93e-02 7.43e+00
        pdb=" CG  TYR E 351 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 351 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 351 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 351 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 351 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 351 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E 351 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 974
        2.82 -     3.34: 2792
        3.34 -     3.86: 5460
        3.86 -     4.38: 5736
        4.38 -     4.90: 9882
  Nonbonded interactions: 24844
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  86 "
            pdb=" OG1 THR A 102 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG1 THR A  74 "
            pdb=" OD1 ASN A  76 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER H  56 "
            pdb=" OG1 THR E 415 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG1 THR E 376 "
            pdb=" NZ  LYS E 378 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" O   ALA A  25 "
            pdb=" OG1 THR A  69 "
     model   vdw
     2.392 3.040
  ... (remaining 24839 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:             3.350
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.970
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   3429  Z= 0.292
  Angle     :  1.292  15.900   4666  Z= 0.687
  Chirality :  0.071   0.500    507
  Planarity :  0.009   0.069    604
  Dihedral  : 13.288  85.060   1224
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.36 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.40 (0.35), residues: 424
  helix: -3.94 (0.49), residues: 33
  sheet: -2.31 (0.46), residues: 100
  loop : -2.14 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 493 
 TYR   0.047   0.003   TYR E 351 
 PHE   0.045   0.003   PHE E 400 
 TRP   0.057   0.006   TRP A  35 
 HIS   0.001   0.000   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 3423)
  covalent geometry    : angle       1.26607 ( 4654)
  SS BOND              : bond        0.01015 (    6)
  SS BOND              : angle       5.25418 (   12)
  hydrogen bonds       : bond        0.25818 (   58)
  hydrogen bonds       : angle      11.14879 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.097 
Fit side-chains
REVERT: H   82 MET cc_start: 0.7811 (mpp) cc_final: 0.7220 (mpp)
REVERT: H  106 MET cc_start: 0.6874 (ptm) cc_final: 0.6642 (ptm)
REVERT: E  389 ASP cc_start: 0.8173 (m-30) cc_final: 0.7776 (p0)
REVERT: E  460 ASN cc_start: 0.8024 (t0) cc_final: 0.7194 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0605
  time to fit residues: 8.4920
Evaluate side-chains
  85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
A  90 GLN
** A 100 GLN ** 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 = 0.3562 r_free = 0.3562 target = 0.091980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.076780 restraints weight = 12805.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.078744 restraints weight = 7846.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.080079 restraints weight = 5595.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081056 restraints weight = 4393.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.081745 restraints weight = 3665.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   3429  Z= 0.291
  Angle     :  0.833  10.600   4666  Z= 0.437
  Chirality :  0.049   0.167    507
  Planarity :  0.006   0.049    604
  Dihedral  :  6.602  31.373    475
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.52 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.36), residues: 424
  helix: -3.07 (0.71), residues: 32
  sheet: -2.21 (0.43), residues: 127
  loop : -2.05 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  38 
 TYR   0.025   0.003   TYR E 380 
 PHE   0.031   0.004   PHE E 392 
 TRP   0.027   0.003   TRP A  35 
 HIS   0.002   0.001   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 3423)
  covalent geometry    : angle       0.81553 ( 4654)
  SS BOND              : bond        0.00898 (    6)
  SS BOND              : angle       3.47049 (   12)
  hydrogen bonds       : bond        0.04919 (   58)
  hydrogen bonds       : angle       8.70430 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   78 LEU cc_start: 0.8784 (tp) cc_final: 0.8559 (tp)
REVERT: H   85 LEU cc_start: 0.8991 (mt) cc_final: 0.8151 (mt)
REVERT: H   86 ARG cc_start: 0.7661 (mmp80) cc_final: 0.7398 (mmp-170)
REVERT: E  460 ASN cc_start: 0.8916 (t0) cc_final: 0.8445 (p0)
REVERT: A    3 GLN cc_start: 0.8060 (mp10) cc_final: 0.7849 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0730
  time to fit residues: 7.7002
Evaluate side-chains
  65 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  53 ASN
** A  89 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.095264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.080965 restraints weight = 11987.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.082931 restraints weight = 7407.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.084198 restraints weight = 5248.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085182 restraints weight = 4121.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.085806 restraints weight = 3433.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3429  Z= 0.158
  Angle     :  0.678   9.689   4666  Z= 0.352
  Chirality :  0.045   0.145    507
  Planarity :  0.005   0.044    604
  Dihedral  :  5.861  30.748    475
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.71 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.37), residues: 424
  helix: -2.95 (0.71), residues: 33
  sheet: -2.15 (0.42), residues: 125
  loop : -1.99 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 355 
 TYR   0.030   0.002   TYR E 380 
 PHE   0.026   0.002   PHE A  71 
 TRP   0.015   0.002   TRP A  35 
 HIS   0.001   0.000   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3423)
  covalent geometry    : angle       0.66348 ( 4654)
  SS BOND              : bond        0.00534 (    6)
  SS BOND              : angle       2.85925 (   12)
  hydrogen bonds       : bond        0.03883 (   58)
  hydrogen bonds       : angle       8.01741 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   85 LEU cc_start: 0.8917 (mt) cc_final: 0.8393 (mt)
REVERT: H   86 ARG cc_start: 0.7765 (mmp80) cc_final: 0.7480 (mmp-170)
REVERT: H  106 MET cc_start: 0.7105 (ptm) cc_final: 0.6819 (ptm)
REVERT: E  461 LEU cc_start: 0.9072 (tp) cc_final: 0.8666 (mt)
REVERT: A    3 GLN cc_start: 0.7940 (mp10) cc_final: 0.7718 (mp10)
  outliers start: 2
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0747
  time to fit residues: 8.0101
Evaluate side-chains
  66 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 11 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4740

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  53 ASN
** A  89 GLN ** 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 = 0.3617 r_free = 0.3617 target = 0.095934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081222 restraints weight = 11563.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.083204 restraints weight = 7076.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.084637 restraints weight = 4984.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.085631 restraints weight = 3846.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.086258 restraints weight = 3187.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3429  Z= 0.135
  Angle     :  0.651   8.852   4666  Z= 0.339
  Chirality :  0.045   0.149    507
  Planarity :  0.005   0.042    604
  Dihedral  :  5.464  29.534    475
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.53 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.37), residues: 424
  helix: -2.68 (0.75), residues: 33
  sheet: -2.06 (0.43), residues: 117
  loop : -1.90 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  38 
 TYR   0.027   0.002   TYR E 380 
 PHE   0.021   0.002   PHE A  98 
 TRP   0.027   0.002   TRP H  36 
 HIS   0.000   0.000   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3423)
  covalent geometry    : angle       0.63556 ( 4654)
  SS BOND              : bond        0.00474 (    6)
  SS BOND              : angle       2.88499 (   12)
  hydrogen bonds       : bond        0.03606 (   58)
  hydrogen bonds       : angle       7.79720 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   20 LEU cc_start: 0.9502 (mt) cc_final: 0.9169 (mp)
REVERT: H   78 LEU cc_start: 0.8792 (tp) cc_final: 0.8429 (tp)
REVERT: H   85 LEU cc_start: 0.8979 (mt) cc_final: 0.8150 (mt)
REVERT: H   86 ARG cc_start: 0.7797 (mmp80) cc_final: 0.7530 (mmp-170)
REVERT: H  103 ASN cc_start: 0.7945 (t0) cc_final: 0.7631 (t0)
REVERT: E  460 ASN cc_start: 0.8842 (t0) cc_final: 0.8365 (p0)
REVERT: A    3 GLN cc_start: 0.8051 (mp10) cc_final: 0.7847 (mp10)
REVERT: A   27 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: A   71 PHE cc_start: 0.8675 (m-80) cc_final: 0.7761 (m-10)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0733
  time to fit residues: 7.7100
Evaluate side-chains
  68 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
** A  89 GLN ** 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 = 0.3581 r_free = 0.3581 target = 0.093879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.079734 restraints weight = 12076.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.081570 restraints weight = 7665.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.082844 restraints weight = 5506.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.083675 restraints weight = 4337.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.084286 restraints weight = 3670.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3429  Z= 0.179
  Angle     :  0.687  10.650   4666  Z= 0.354
  Chirality :  0.046   0.144    507
  Planarity :  0.005   0.042    604
  Dihedral  :  5.616  29.953    475
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.38), residues: 424
  helix: -2.64 (0.78), residues: 33
  sheet: -2.33 (0.41), residues: 127
  loop : -1.74 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.021   0.002   TYR E 380 
 PHE   0.031   0.003   PHE E 392 
 TRP   0.017   0.002   TRP H  36 
 HIS   0.000   0.000   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3423)
  covalent geometry    : angle       0.66534 ( 4654)
  SS BOND              : bond        0.00433 (    6)
  SS BOND              : angle       3.45454 (   12)
  hydrogen bonds       : bond        0.03623 (   58)
  hydrogen bonds       : angle       7.52040 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   33 TYR cc_start: 0.7071 (m-10) cc_final: 0.6539 (m-10)
REVERT: H   78 LEU cc_start: 0.8704 (tp) cc_final: 0.8363 (tp)
REVERT: H   85 LEU cc_start: 0.9127 (mt) cc_final: 0.8763 (mt)
REVERT: H   86 ARG cc_start: 0.8009 (mmp80) cc_final: 0.7634 (mmp-170)
REVERT: H  103 ASN cc_start: 0.7864 (t0) cc_final: 0.7559 (t0)
REVERT: E  421 TYR cc_start: 0.7961 (m-80) cc_final: 0.7672 (m-10)
REVERT: E  460 ASN cc_start: 0.8893 (t0) cc_final: 0.8667 (t0)
REVERT: E  461 LEU cc_start: 0.8968 (tp) cc_final: 0.8444 (mt)
REVERT: A   27 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: A   71 PHE cc_start: 0.8634 (m-80) cc_final: 0.7799 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0723
  time to fit residues: 7.5899
Evaluate side-chains
  67 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0470
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
E 370 ASN
A   6 GLN
A  53 ASN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.093676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.078907 restraints weight = 11938.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080828 restraints weight = 7311.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.082193 restraints weight = 5186.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.083156 restraints weight = 4027.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.083752 restraints weight = 3360.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3429  Z= 0.171
  Angle     :  0.681  10.010   4666  Z= 0.351
  Chirality :  0.045   0.144    507
  Planarity :  0.004   0.046    604
  Dihedral  :  5.484  27.971    475
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.43 %
    Favored  : 94.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.38), residues: 424
  helix: -2.56 (0.79), residues: 34
  sheet: -2.14 (0.42), residues: 132
  loop : -1.85 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  97 
 TYR   0.021   0.002   TYR E 380 
 PHE   0.016   0.002   PHE A  71 
 TRP   0.010   0.002   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3423)
  covalent geometry    : angle       0.66605 ( 4654)
  SS BOND              : bond        0.00473 (    6)
  SS BOND              : angle       2.90070 (   12)
  hydrogen bonds       : bond        0.03627 (   58)
  hydrogen bonds       : angle       7.52848 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   78 LEU cc_start: 0.8706 (tp) cc_final: 0.8374 (tp)
REVERT: H   85 LEU cc_start: 0.9158 (mt) cc_final: 0.8923 (mt)
REVERT: H   86 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7658 (mmp-170)
REVERT: H  103 ASN cc_start: 0.7906 (t0) cc_final: 0.7575 (t0)
REVERT: E  461 LEU cc_start: 0.9011 (tp) cc_final: 0.8705 (mt)
REVERT: A   27 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: A   50 ASP cc_start: 0.9034 (t0) cc_final: 0.8819 (t0)
REVERT: A   70 ASP cc_start: 0.9267 (m-30) cc_final: 0.9051 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 92
  average time/residue: 0.0741
  time to fit residues: 8.1576
Evaluate side-chains
  74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0370
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0020
   chunk 24 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.2866

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  53 ASN
** A  89 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.096789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.082037 restraints weight = 12044.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.084021 restraints weight = 7311.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.085459 restraints weight = 5129.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.086438 restraints weight = 3930.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.087160 restraints weight = 3255.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3429  Z= 0.122
  Angle     :  0.703  10.591   4666  Z= 0.357
  Chirality :  0.046   0.173    507
  Planarity :  0.004   0.045    604
  Dihedral  :  5.144  27.110    475
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.38), residues: 424
  helix: -2.60 (0.75), residues: 35
  sheet: -2.08 (0.42), residues: 123
  loop : -1.84 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 408 
 TYR   0.025   0.001   TYR E 380 
 PHE   0.014   0.002   PHE A  98 
 TRP   0.015   0.002   TRP H  36 
 HIS   0.000   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3423)
  covalent geometry    : angle       0.66427 ( 4654)
  SS BOND              : bond        0.00180 (    6)
  SS BOND              : angle       4.59338 (   12)
  hydrogen bonds       : bond        0.03134 (   58)
  hydrogen bonds       : angle       7.13428 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   33 TYR cc_start: 0.7268 (m-10) cc_final: 0.6738 (m-10)
REVERT: H   85 LEU cc_start: 0.9060 (mt) cc_final: 0.8721 (mt)
REVERT: H   86 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7499 (mmp-170)
REVERT: H  103 ASN cc_start: 0.7852 (t0) cc_final: 0.7635 (t0)
REVERT: E  417 ASN cc_start: 0.7930 (p0) cc_final: 0.7500 (p0)
REVERT: E  418 ILE cc_start: 0.8549 (mp) cc_final: 0.8347 (mp)
REVERT: E  421 TYR cc_start: 0.7890 (m-80) cc_final: 0.7443 (m-10)
REVERT: E  489 TYR cc_start: 0.5802 (m-80) cc_final: 0.5473 (m-80)
REVERT: A   27 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: A   70 ASP cc_start: 0.9210 (m-30) cc_final: 0.8998 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0816
  time to fit residues: 9.5573
Evaluate side-chains
  74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
E 370 ASN
A  53 ASN
** A  89 GLN ** 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 = 0.095238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.080685 restraints weight = 12226.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082634 restraints weight = 7632.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.083976 restraints weight = 5394.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.084939 restraints weight = 4197.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085366 restraints weight = 3488.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3429  Z= 0.162
  Angle     :  0.717  10.899   4666  Z= 0.368
  Chirality :  0.046   0.161    507
  Planarity :  0.004   0.047    604
  Dihedral  :  5.383  27.967    475
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.36 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.38), residues: 424
  helix: -2.70 (0.74), residues: 35
  sheet: -2.21 (0.44), residues: 118
  loop : -1.87 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  97 
 TYR   0.020   0.002   TYR E 380 
 PHE   0.021   0.002   PHE E 392 
 TRP   0.034   0.002   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3423)
  covalent geometry    : angle       0.69395 ( 4654)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       3.63234 (   12)
  hydrogen bonds       : bond        0.03729 (   58)
  hydrogen bonds       : angle       7.43880 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   33 TYR cc_start: 0.6240 (m-10) cc_final: 0.5613 (m-10)
REVERT: H   78 LEU cc_start: 0.8850 (tp) cc_final: 0.8497 (tp)
REVERT: H   85 LEU cc_start: 0.9020 (mt) cc_final: 0.8709 (mt)
REVERT: H   86 ARG cc_start: 0.8052 (mmp80) cc_final: 0.7529 (mmp-170)
REVERT: E  417 ASN cc_start: 0.8068 (p0) cc_final: 0.7544 (p0)
REVERT: E  418 ILE cc_start: 0.8670 (mp) cc_final: 0.8412 (mp)
REVERT: E  421 TYR cc_start: 0.7889 (m-80) cc_final: 0.7519 (m-10)
REVERT: A   27 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: A   70 ASP cc_start: 0.9200 (m-30) cc_final: 0.8996 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0665
  time to fit residues: 7.2469
Evaluate side-chains
  69 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 18 optimal weight:    0.2980
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0670
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A  89 GLN ** 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 = 0.3615 r_free = 0.3615 target = 0.095825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081451 restraints weight = 12058.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.083333 restraints weight = 7647.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.084629 restraints weight = 5471.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.085477 restraints weight = 4310.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.085920 restraints weight = 3648.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3429  Z= 0.148
  Angle     :  0.716  10.585   4666  Z= 0.368
  Chirality :  0.046   0.149    507
  Planarity :  0.004   0.047    604
  Dihedral  :  5.397  27.617    475
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.38), residues: 424
  helix: -2.67 (0.74), residues: 35
  sheet: -2.20 (0.44), residues: 119
  loop : -1.78 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 408 
 TYR   0.021   0.001   TYR E 380 
 PHE   0.021   0.002   PHE E 456 
 TRP   0.029   0.002   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3423)
  covalent geometry    : angle       0.69749 ( 4654)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       3.24502 (   12)
  hydrogen bonds       : bond        0.03420 (   58)
  hydrogen bonds       : angle       7.39686 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   33 TYR cc_start: 0.6688 (m-10) cc_final: 0.6140 (m-10)
REVERT: H   78 LEU cc_start: 0.8862 (tp) cc_final: 0.8395 (tp)
REVERT: H   85 LEU cc_start: 0.9042 (mt) cc_final: 0.8335 (mt)
REVERT: H   86 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7489 (mmp-170)
REVERT: E  417 ASN cc_start: 0.7908 (p0) cc_final: 0.7459 (p0)
REVERT: E  418 ILE cc_start: 0.8667 (mp) cc_final: 0.8365 (mp)
REVERT: E  421 TYR cc_start: 0.7948 (m-80) cc_final: 0.7628 (m-10)
REVERT: A   27 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8318 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0678
  time to fit residues: 7.5660
Evaluate side-chains
  71 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0000
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A  89 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.094876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.080567 restraints weight = 12032.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.082488 restraints weight = 7470.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.083846 restraints weight = 5293.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.084760 restraints weight = 4117.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.085429 restraints weight = 3436.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3429  Z= 0.162
  Angle     :  0.731  10.523   4666  Z= 0.376
  Chirality :  0.046   0.151    507
  Planarity :  0.004   0.047    604
  Dihedral  :  5.522  27.992    475
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.38), residues: 424
  helix: -2.61 (0.78), residues: 33
  sheet: -2.21 (0.44), residues: 119
  loop : -1.89 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 408 
 TYR   0.019   0.002   TYR E 380 
 PHE   0.021   0.002   PHE E 392 
 TRP   0.030   0.002   TRP H  36 
 HIS   0.000   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3423)
  covalent geometry    : angle       0.71320 ( 4654)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       3.23357 (   12)
  hydrogen bonds       : bond        0.03571 (   58)
  hydrogen bonds       : angle       7.39796 (  156)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   20 LEU cc_start: 0.9589 (mt) cc_final: 0.9332 (mp)
REVERT: H   33 TYR cc_start: 0.6512 (m-10) cc_final: 0.5850 (m-10)
REVERT: H   78 LEU cc_start: 0.8761 (tp) cc_final: 0.8316 (tp)
REVERT: H   85 LEU cc_start: 0.8993 (mt) cc_final: 0.8763 (mt)
REVERT: H   86 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7403 (mmp-170)
REVERT: H  103 ASN cc_start: 0.7934 (t0) cc_final: 0.7617 (t0)
REVERT: E  417 ASN cc_start: 0.7853 (p0) cc_final: 0.7404 (p0)
REVERT: E  418 ILE cc_start: 0.8647 (mp) cc_final: 0.8344 (mp)
REVERT: E  421 TYR cc_start: 0.7930 (m-80) cc_final: 0.7539 (m-10)
REVERT: A    4 MET cc_start: 0.7671 (tpt) cc_final: 0.7434 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0747
  time to fit residues: 8.2644
Evaluate side-chains
  72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A  89 GLN ** 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 = 0.3598 r_free = 0.3598 target = 0.095224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.080447 restraints weight = 12317.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.082476 restraints weight = 7546.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.083857 restraints weight = 5315.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.084824 restraints weight = 4128.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.085344 restraints weight = 3446.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3429  Z= 0.174
  Angle     :  0.784  10.695   4666  Z= 0.399
  Chirality :  0.047   0.146    507
  Planarity :  0.004   0.046    604
  Dihedral  :  5.623  28.144    475
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.38), residues: 424
  helix: -2.55 (0.79), residues: 33
  sheet: -2.31 (0.44), residues: 121
  loop : -1.84 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  97 
 TYR   0.018   0.002   TYR E 380 
 PHE   0.028   0.003   PHE E 456 
 TRP   0.033   0.002   TRP H  36 
 HIS   0.000   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3423)
  covalent geometry    : angle       0.75025 ( 4654)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       4.55983 (   12)
  hydrogen bonds       : bond        0.03579 (   58)
  hydrogen bonds       : angle       7.48101 (  156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 866.75 seconds
wall clock time: 15 minutes 37.66 seconds (937.66 seconds total)