Starting phenix.real_space_refine
on Fri Aug 22 14:36:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nnf_49573/08_2025/9nnf_49573.map"
  }
  resolution = 3.8
  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=   0.024
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      19      5.16       5
     C    2627      2.51       5
     N     750      2.21       5
     O     789      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4185
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1021
          Classifications: {'peptide': 141}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2253
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 12, 'TRANS': 263}
    Chain: "C"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 836
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 75
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 1.06, per 1000 atoms: 0.25
  Number of scatterers: 4185
  At special positions: 0
  Unit cell: (62.466, 73.236, 104.11, 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      19     16.00
     O     789      8.00
     N     750      7.00
     C    2627      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 246 " - pdb=" SG  CYS B 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 348 " - pdb=" SG  CYS B 404 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 447 " - pdb=" SG  CYS C 502 " distance=2.04

  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: 0.33
  Conformation dependent library (CDL) restraints added in 160.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  996

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 6 sheets defined
      38.0% alpha, 24.9% 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 10 through 25
      removed outlier: 3.852A  pdb=" N   ALA A  14 " --> pdb=" O   ALA A  10 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ARG A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 51
    Processing helix  chain 'A' and resid 58 through 84
    Processing helix  chain 'A' and resid 87 through 110
    Processing helix  chain 'A' and resid 112 through 145
      removed outlier: 4.372A  pdb=" N   GLN A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLN A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 231
      removed outlier: 3.623A  pdb=" N   TRP B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 295
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 307 through 320
    Processing helix  chain 'B' and resid 320 through 325
    Processing sheet with id=AA1, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.593A  pdb=" N   GLU B 191 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLY B 171 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ARG B 180 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ALA B 169 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG B 256 " --> pdb=" O   ASP B 247 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   HIS B 259 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339
    Processing sheet with id=AA3, first strand: chain 'B' and resid 333 through 339
    Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 363
    Processing sheet with id=AA5, first strand: chain 'C' and resid 429 through 433
    Processing sheet with id=AA6, first strand: chain 'C' and resid 457 through 463

    256 hydrogen bonds defined for protein.
    726 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: 0.64

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1420
        1.34 -     1.46: 991
        1.46 -     1.58: 1843
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 4285
  Sorted by residual:
  bond pdb=" CA  ASP C 520 "
       pdb=" CB  ASP C 520 "
    ideal  model  delta    sigma   weight residual
    1.528  1.556 -0.028 2.61e-02 1.47e+03 1.15e+00
  bond pdb=" CB  ARG B 210 "
       pdb=" CG  ARG B 210 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CB  VAL B 212 "
       pdb=" CG2 VAL B 212 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" CB  ARG A  25 "
       pdb=" CG  ARG A  25 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.81e-01
  bond pdb=" CG  LEU D 523 "
       pdb=" CD1 LEU D 523 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.92e-01
  ... (remaining 4280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 5647
        1.93 -     3.87: 142
        3.87 -     5.80: 17
        5.80 -     7.74: 4
        7.74 -     9.67: 2
  Bond angle restraints: 5812
  Sorted by residual:
  angle pdb=" N   PHE C 452 "
        pdb=" CA  PHE C 452 "
        pdb=" C   PHE C 452 "
      ideal   model   delta    sigma   weight residual
     110.80  119.27   -8.47 2.13e+00 2.20e-01 1.58e+01
  angle pdb=" C   PHE C 452 "
        pdb=" N   HIS C 453 "
        pdb=" CA  HIS C 453 "
      ideal   model   delta    sigma   weight residual
     121.80  112.13    9.67 2.44e+00 1.68e-01 1.57e+01
  angle pdb=" C   TYR A 107 "
        pdb=" N   VAL A 108 "
        pdb=" CA  VAL A 108 "
      ideal   model   delta    sigma   weight residual
     120.60  125.13   -4.53 1.29e+00 6.01e-01 1.23e+01
  angle pdb=" C   ALA A 144 "
        pdb=" N   ARG A 145 "
        pdb=" CA  ARG A 145 "
      ideal   model   delta    sigma   weight residual
     121.70  126.15   -4.45 1.80e+00 3.09e-01 6.10e+00
  angle pdb=" C   PHE C 452 "
        pdb=" CA  PHE C 452 "
        pdb=" CB  PHE C 452 "
      ideal   model   delta    sigma   weight residual
     110.42  105.99    4.43 1.99e+00 2.53e-01 4.96e+00
  ... (remaining 5807 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.79: 2335
       15.79 -    31.59: 178
       31.59 -    47.38: 39
       47.38 -    63.18: 6
       63.18 -    78.97: 3
  Dihedral angle restraints: 2561
    sinusoidal: 1023
      harmonic: 1538
  Sorted by residual:
  dihedral pdb=" CA  MET B 243 "
           pdb=" C   MET B 243 "
           pdb=" N   TYR B 244 "
           pdb=" CA  TYR B 244 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.12   17.88     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  GLY C 451 "
           pdb=" C   GLY C 451 "
           pdb=" N   PHE C 452 "
           pdb=" CA  PHE C 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.29   17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  TYR B 172 "
           pdb=" C   TYR B 172 "
           pdb=" N   VAL B 173 "
           pdb=" CA  VAL B 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.23   16.77     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 2558 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 444
       0.042 -    0.084: 139
       0.084 -    0.126: 31
       0.126 -    0.168: 5
       0.168 -    0.210: 2
  Chirality restraints: 621
  Sorted by residual:
  chirality pdb=" CA  PHE C 452 "
            pdb=" N   PHE C 452 "
            pdb=" C   PHE C 452 "
            pdb=" CB  PHE C 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  THR A 125 "
            pdb=" CA  THR A 125 "
            pdb=" OG1 THR A 125 "
            pdb=" CG2 THR A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.23e-01
  chirality pdb=" CB  ILE D 527 "
            pdb=" CA  ILE D 527 "
            pdb=" CG1 ILE D 527 "
            pdb=" CG2 ILE D 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.45e-01
  ... (remaining 618 not shown)

  Planarity restraints: 759
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  83 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.08e+00
        pdb=" C   VAL A  83 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A  83 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A  84 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 229 "    0.013 2.00e-02 2.50e+03   1.28e-02 3.26e+00
        pdb=" CG  TYR B 229 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 229 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 229 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 229 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 229 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 229 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 229 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 394 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 395 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 395 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 395 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 756 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 2184
        3.02 -     3.49: 4203
        3.49 -     3.96: 6431
        3.96 -     4.43: 7572
        4.43 -     4.90: 12293
  Nonbonded interactions: 32683
  Sorted by model distance:
  nonbonded pdb=" O   PHE C 452 "
            pdb=" CA  HIS C 453 "
     model   vdw
     2.553 2.776
  nonbonded pdb=" O   PHE C 452 "
            pdb=" CB  PHE C 452 "
     model   vdw
     2.577 2.752
  nonbonded pdb=" N   HIS B 333 "
            pdb=" O   HIS B 333 "
     model   vdw
     2.625 2.496
  nonbonded pdb=" N   PHE C 492 "
            pdb=" O   PHE C 492 "
     model   vdw
     2.646 2.496
  nonbonded pdb=" N   HIS B 337 "
            pdb=" O   HIS B 337 "
     model   vdw
     2.647 2.496
  ... (remaining 32678 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.270
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4288  Z= 0.167
  Angle     :  0.720   9.669   5818  Z= 0.377
  Chirality :  0.044   0.210    621
  Planarity :  0.006   0.045    759
  Dihedral  : 12.253  78.970   1556
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.37), residues: 516
  helix:  1.87 (0.36), residues: 193
  sheet: -0.26 (0.46), residues: 134
  loop : -1.00 (0.44), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 193 
 TYR   0.032   0.003   TYR B 229 
 PHE   0.024   0.003   PHE C 452 
 TRP   0.010   0.001   TRP C 517 
 HIS   0.008   0.002   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4285)
  covalent geometry    : angle       0.71974 ( 5812)
  SS BOND              : bond        0.00353 (    3)
  SS BOND              : angle       0.91621 (    6)
  hydrogen bonds       : bond        0.10476 (  240)
  hydrogen bonds       : angle       5.49075 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 ASP cc_start: 0.8711 (m-30) cc_final: 0.8509 (m-30)
REVERT: B  199 GLN cc_start: 0.7876 (mp10) cc_final: 0.7083 (mp10)
REVERT: B  253 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7079 (mmm-85)
REVERT: B  261 TYR cc_start: 0.8804 (t80) cc_final: 0.8585 (t80)
REVERT: B  291 LYS cc_start: 0.8532 (tttt) cc_final: 0.7835 (ttmm)
REVERT: B  318 GLU cc_start: 0.7436 (tp30) cc_final: 0.7139 (tp30)
REVERT: B  319 ASN cc_start: 0.8513 (t0) cc_final: 0.6994 (t0)
REVERT: C  505 ASN cc_start: 0.8443 (t0) cc_final: 0.8130 (t0)
REVERT: C  516 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8257 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0894
  time to fit residues: 13.7815
Evaluate side-chains
  92 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   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 110 HIS
** D 529 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 = 0.3708 r_free = 0.3708 target = 0.161869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.126630 restraints weight = 4968.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.130540 restraints weight = 4507.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.131023 restraints weight = 3157.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.131319 restraints weight = 2545.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.131665 restraints weight = 2370.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4288  Z= 0.132
  Angle     :  0.555   9.098   5818  Z= 0.289
  Chirality :  0.038   0.136    621
  Planarity :  0.004   0.040    759
  Dihedral  :  4.345  17.549    582
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.35 %
    Favored  : 88.24 %
  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:  0.90 (0.38), residues: 516
  helix:  2.39 (0.36), residues: 195
  sheet: -0.03 (0.45), residues: 133
  loop : -0.84 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 503 
 TYR   0.025   0.002   TYR B 229 
 PHE   0.015   0.002   PHE C 484 
 TRP   0.008   0.001   TRP B 278 
 HIS   0.006   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4285)
  covalent geometry    : angle       0.55511 ( 5812)
  SS BOND              : bond        0.00027 (    3)
  SS BOND              : angle       0.53937 (    6)
  hydrogen bonds       : bond        0.03952 (  240)
  hydrogen bonds       : angle       4.21442 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7661 (mpt90)
REVERT: A  142 LEU cc_start: 0.8929 (tp) cc_final: 0.8714 (tt)
REVERT: B  199 GLN cc_start: 0.7747 (mp10) cc_final: 0.7480 (mp10)
REVERT: B  291 LYS cc_start: 0.8413 (tttt) cc_final: 0.7804 (ttmm)
REVERT: C  424 GLN cc_start: 0.8613 (pm20) cc_final: 0.8027 (mp10)
REVERT: C  516 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8221 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0726
  time to fit residues: 8.6872
Evaluate side-chains
  88 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  450 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    0.0980
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 41 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
B 319 ASN
** D 529 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 = 0.3702 r_free = 0.3702 target = 0.161598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.127254 restraints weight = 5021.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.127984 restraints weight = 4360.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.130139 restraints weight = 3586.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.130279 restraints weight = 2478.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.131782 restraints weight = 2288.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4288  Z= 0.122
  Angle     :  0.528   8.808   5818  Z= 0.276
  Chirality :  0.037   0.128    621
  Planarity :  0.004   0.038    759
  Dihedral  :  4.201  18.396    582
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.29 %
    Favored  : 86.35 %
  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:  1.07 (0.38), residues: 516
  helix:  2.50 (0.37), residues: 195
  sheet:  0.13 (0.45), residues: 133
  loop : -0.76 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 141 
 TYR   0.018   0.002   TYR B 229 
 PHE   0.012   0.001   PHE B 178 
 TRP   0.007   0.001   TRP B 349 
 HIS   0.006   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4285)
  covalent geometry    : angle       0.52853 ( 5812)
  SS BOND              : bond        0.00061 (    3)
  SS BOND              : angle       0.42725 (    6)
  hydrogen bonds       : bond        0.03844 (  240)
  hydrogen bonds       : angle       3.96264 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.7917 (p0) cc_final: 0.7628 (p0)
REVERT: A  142 LEU cc_start: 0.8949 (tp) cc_final: 0.8747 (tt)
REVERT: B  199 GLN cc_start: 0.7616 (mp10) cc_final: 0.7396 (mp10)
REVERT: B  291 LYS cc_start: 0.8412 (tttt) cc_final: 0.7664 (ttmm)
REVERT: C  434 ARG cc_start: 0.8416 (ttm170) cc_final: 0.7698 (ttm-80)
REVERT: C  516 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8300 (mtpp)
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0884
  time to fit residues: 10.3287
Evaluate side-chains
  88 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain C residue  475 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 119 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 = 0.3681 r_free = 0.3681 target = 0.159448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.124967 restraints weight = 4982.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.124718 restraints weight = 4799.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.125887 restraints weight = 4463.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.126335 restraints weight = 3448.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.127668 restraints weight = 3130.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4288  Z= 0.125
  Angle     :  0.520   8.891   5818  Z= 0.274
  Chirality :  0.037   0.131    621
  Planarity :  0.004   0.038    759
  Dihedral  :  4.114  19.505    582
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.65 %
    Favored  : 83.29 %
  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:  1.15 (0.38), residues: 516
  helix:  2.58 (0.37), residues: 195
  sheet:  0.19 (0.45), residues: 135
  loop : -0.76 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 276 
 TYR   0.016   0.002   TYR C 485 
 PHE   0.012   0.001   PHE B 178 
 TRP   0.006   0.001   TRP D 526 
 HIS   0.007   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4285)
  covalent geometry    : angle       0.52033 ( 5812)
  SS BOND              : bond        0.00050 (    3)
  SS BOND              : angle       0.34293 (    6)
  hydrogen bonds       : bond        0.03663 (  240)
  hydrogen bonds       : angle       3.85298 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B  199 GLN cc_start: 0.7548 (mp10) cc_final: 0.7306 (mt0)
REVERT: B  291 LYS cc_start: 0.8430 (tttt) cc_final: 0.7707 (ttmm)
REVERT: B  318 GLU cc_start: 0.7431 (tp30) cc_final: 0.7046 (tp30)
REVERT: C  424 GLN cc_start: 0.8710 (pm20) cc_final: 0.8382 (pm20)
REVERT: C  516 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8316 (mtpp)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0855
  time to fit residues: 10.5171
Evaluate side-chains
  92 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain C residue  475 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0010
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
** A 119 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 = 0.3640 r_free = 0.3640 target = 0.156483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.124598 restraints weight = 4919.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.125345 restraints weight = 5588.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125873 restraints weight = 4535.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.126363 restraints weight = 3758.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.127310 restraints weight = 3248.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4288  Z= 0.138
  Angle     :  0.529   9.639   5818  Z= 0.276
  Chirality :  0.038   0.132    621
  Planarity :  0.004   0.034    759
  Dihedral  :  4.133  20.417    582
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.06 %
    Favored  : 81.65 %
  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:  1.16 (0.38), residues: 516
  helix:  2.56 (0.37), residues: 196
  sheet:  0.17 (0.45), residues: 135
  loop : -0.71 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  70 
 TYR   0.017   0.002   TYR C 485 
 PHE   0.010   0.001   PHE B 178 
 TRP   0.007   0.001   TRP D 526 
 HIS   0.008   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4285)
  covalent geometry    : angle       0.52901 ( 5812)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       0.29926 (    6)
  hydrogen bonds       : bond        0.03654 (  240)
  hydrogen bonds       : angle       3.87627 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B  199 GLN cc_start: 0.7480 (mp10) cc_final: 0.7265 (mt0)
REVERT: B  291 LYS cc_start: 0.8393 (tttt) cc_final: 0.7664 (ttmm)
REVERT: B  318 GLU cc_start: 0.7393 (tp30) cc_final: 0.7015 (tp30)
REVERT: C  516 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8392 (mtpp)
  outliers start: 14
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0674
  time to fit residues: 8.5903
Evaluate side-chains
  92 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain C residue  475 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.156830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.124241 restraints weight = 5056.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.124327 restraints weight = 5343.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125653 restraints weight = 5006.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125879 restraints weight = 3972.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.127309 restraints weight = 3522.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4288  Z= 0.129
  Angle     :  0.553   8.365   5818  Z= 0.284
  Chirality :  0.038   0.136    621
  Planarity :  0.004   0.031    759
  Dihedral  :  4.134  21.207    582
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.47 %
    Favored  : 80.24 %
  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:  1.17 (0.38), residues: 516
  helix:  2.61 (0.37), residues: 196
  sheet:  0.18 (0.45), residues: 135
  loop : -0.78 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.014   0.002   TYR B 244 
 PHE   0.016   0.001   PHE B 178 
 TRP   0.006   0.001   TRP B 349 
 HIS   0.007   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4285)
  covalent geometry    : angle       0.55349 ( 5812)
  SS BOND              : bond        0.00053 (    3)
  SS BOND              : angle       0.27399 (    6)
  hydrogen bonds       : bond        0.03576 (  240)
  hydrogen bonds       : angle       3.82579 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B  291 LYS cc_start: 0.8394 (tttt) cc_final: 0.7665 (ttmm)
REVERT: B  318 GLU cc_start: 0.7402 (tp30) cc_final: 0.7040 (tp30)
REVERT: C  516 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8358 (mtpp)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0633
  time to fit residues: 7.6111
Evaluate side-chains
  87 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0980

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.154965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.123017 restraints weight = 5056.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.122212 restraints weight = 5351.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.123581 restraints weight = 5455.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.123907 restraints weight = 4105.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.124997 restraints weight = 3720.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4288  Z= 0.152
  Angle     :  0.579   9.432   5818  Z= 0.295
  Chirality :  0.039   0.194    621
  Planarity :  0.004   0.031    759
  Dihedral  :  4.220  22.370    582
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.24 %
    Favored  : 80.24 %
  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:  1.17 (0.38), residues: 516
  helix:  2.59 (0.37), residues: 196
  sheet:  0.17 (0.45), residues: 135
  loop : -0.74 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  25 
 TYR   0.014   0.002   TYR C 485 
 PHE   0.013   0.001   PHE B 178 
 TRP   0.006   0.001   TRP C 482 
 HIS   0.008   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4285)
  covalent geometry    : angle       0.57940 ( 5812)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       0.25827 (    6)
  hydrogen bonds       : bond        0.03631 (  240)
  hydrogen bonds       : angle       3.85673 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7746 (pm20)
REVERT: B  291 LYS cc_start: 0.8445 (tttt) cc_final: 0.7784 (ttmm)
REVERT: B  318 GLU cc_start: 0.7379 (tp30) cc_final: 0.6996 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0619
  time to fit residues: 7.3827
Evaluate side-chains
  89 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.156619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.122683 restraints weight = 5046.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125618 restraints weight = 4464.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.126195 restraints weight = 3370.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.126641 restraints weight = 2697.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.126953 restraints weight = 2463.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4288  Z= 0.158
  Angle     :  0.581   9.449   5818  Z= 0.301
  Chirality :  0.039   0.146    621
  Planarity :  0.004   0.030    759
  Dihedral  :  4.294  23.381    582
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.18 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.38), residues: 516
  helix:  2.54 (0.37), residues: 196
  sheet:  0.15 (0.45), residues: 135
  loop : -0.70 (0.46), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.018   0.002   TYR B 229 
 PHE   0.013   0.001   PHE B 178 
 TRP   0.006   0.001   TRP C 482 
 HIS   0.008   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4285)
  covalent geometry    : angle       0.58078 ( 5812)
  SS BOND              : bond        0.00065 (    3)
  SS BOND              : angle       0.33933 (    6)
  hydrogen bonds       : bond        0.03637 (  240)
  hydrogen bonds       : angle       3.87974 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7813 (pm20)
REVERT: B  291 LYS cc_start: 0.8507 (tttt) cc_final: 0.7793 (ttmm)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0632
  time to fit residues: 7.4857
Evaluate side-chains
  93 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 48 optimal weight:    0.3980
   chunk 14 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.160594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.127394 restraints weight = 5070.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.128679 restraints weight = 4207.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.130045 restraints weight = 4015.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.130502 restraints weight = 2787.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.131656 restraints weight = 2507.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4288  Z= 0.114
  Angle     :  0.547   7.250   5818  Z= 0.286
  Chirality :  0.037   0.138    621
  Planarity :  0.004   0.032    759
  Dihedral  :  4.135  22.610    582
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.35 %
    Favored  : 79.29 %
  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:  1.20 (0.38), residues: 516
  helix:  2.63 (0.37), residues: 196
  sheet:  0.21 (0.44), residues: 136
  loop : -0.76 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.018   0.001   TYR B 229 
 PHE   0.014   0.001   PHE B 178 
 TRP   0.008   0.001   TRP B 349 
 HIS   0.004   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4285)
  covalent geometry    : angle       0.54691 ( 5812)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       0.44705 (    6)
  hydrogen bonds       : bond        0.03396 (  240)
  hydrogen bonds       : angle       3.77023 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7802 (pm20)
REVERT: B  199 GLN cc_start: 0.7472 (pm20) cc_final: 0.7201 (pt0)
REVERT: B  291 LYS cc_start: 0.8501 (tttt) cc_final: 0.7787 (ttmm)
REVERT: C  516 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8057 (mmtt)
  outliers start: 10
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0763
  time to fit residues: 8.4513
Evaluate side-chains
  89 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0050
   chunk 2 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** D 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.159591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.127566 restraints weight = 5030.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.129009 restraints weight = 4620.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.130015 restraints weight = 3402.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.130347 restraints weight = 2729.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.130561 restraints weight = 2539.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4288  Z= 0.131
  Angle     :  0.582   8.852   5818  Z= 0.300
  Chirality :  0.038   0.135    621
  Planarity :  0.004   0.030    759
  Dihedral  :  4.106  21.938    582
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.06 %
    Favored  : 78.82 %
  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:  1.21 (0.38), residues: 516
  helix:  2.66 (0.36), residues: 196
  sheet:  0.24 (0.45), residues: 135
  loop : -0.81 (0.46), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  25 
 TYR   0.016   0.002   TYR B 229 
 PHE   0.014   0.001   PHE B 178 
 TRP   0.007   0.001   TRP B 362 
 HIS   0.006   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4285)
  covalent geometry    : angle       0.58174 ( 5812)
  SS BOND              : bond        0.00053 (    3)
  SS BOND              : angle       0.41863 (    6)
  hydrogen bonds       : bond        0.03444 (  240)
  hydrogen bonds       : angle       3.75062 (  726)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7718 (pm20)
REVERT: B  291 LYS cc_start: 0.8452 (tttt) cc_final: 0.7744 (ttmm)
REVERT: C  516 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8089 (mmtt)
  outliers start: 9
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0721
  time to fit residues: 8.0291
Evaluate side-chains
  91 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 ASN
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain C residue  426 THR
Chi-restraints excluded: chain C residue  442 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0570
   chunk 0 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 39 optimal weight:   30.0000
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.160426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.127639 restraints weight = 5085.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.127547 restraints weight = 4632.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.128726 restraints weight = 3736.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.129200 restraints weight = 2927.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.129714 restraints weight = 2752.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4288  Z= 0.123
  Angle     :  0.569   8.091   5818  Z= 0.296
  Chirality :  0.038   0.133    621
  Planarity :  0.004   0.031    759
  Dihedral  :  4.095  22.380    582
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.76 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.38), residues: 516
  helix:  2.66 (0.36), residues: 196
  sheet:  0.35 (0.45), residues: 134
  loop : -0.87 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.016   0.001   TYR B 229 
 PHE   0.014   0.001   PHE B 178 
 TRP   0.007   0.001   TRP B 349 
 HIS   0.005   0.001   HIS C 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4285)
  covalent geometry    : angle       0.56923 ( 5812)
  SS BOND              : bond        0.00052 (    3)
  SS BOND              : angle       0.38777 (    6)
  hydrogen bonds       : bond        0.03395 (  240)
  hydrogen bonds       : angle       3.73849 (  726)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 806.71 seconds
wall clock time: 14 minutes 31.31 seconds (871.31 seconds total)