Starting phenix.real_space_refine
on Tue Aug  4 14:36:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/26vd_80906/08_2026/26vd_80906.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/26vd_80906/08_2026/26vd_80906.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/26vd_80906/08_2026/26vd_80906.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/26vd_80906/08_2026/26vd_80906.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/26vd_80906/08_2026/26vd_80906.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/26vd_80906/08_2026/26vd_80906.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=   0.001 sd=   0.011
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      32      5.16       5
     C    2597      2.51       5
     N     621      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3906
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3906
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 22, 'TRANS': 485}
          Chain breaks: 1
  Time building chain proxies: 1.00, per 1000 atoms: 0.26
  Number of scatterers: 3906
  At special positions: 0
  Unit cell: (78.85, 63.08, 75.53, 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      32     16.00
     O     656      8.00
     N     621      7.00
     C    2597      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.32
  Conformation dependent library (CDL) restraints added in 179.3 milliseconds
  

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  916

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      85.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 49
    Processing helix  chain 'A' and resid 55 through 62
    Processing helix  chain 'A' and resid 63 through 65
      No H-bonds generated for 'chain 'A' and resid 63 through 65'
    Processing helix  chain 'A' and resid 67 through 80
      removed outlier: 4.128A  pdb=" N   PHE A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 96
      Proline residue:  A  89  - end of helix
    Processing helix  chain 'A' and resid 97 through 104
    Processing helix  chain 'A' and resid 105 through 112
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 129 through 135
      removed outlier: 3.695A  pdb=" N   LEU A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 173
      removed outlier: 3.790A  pdb=" N   ARG A 142 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 158 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   VAL A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
    Processing helix  chain 'A' and resid 175 through 195
    Processing helix  chain 'A' and resid 195 through 226
    Processing helix  chain 'A' and resid 227 through 238
    Processing helix  chain 'A' and resid 255 through 272
      removed outlier: 4.061A  pdb=" N   PHE A 261 " --> pdb=" O   TRP A 257 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   VAL A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 282
      removed outlier: 3.652A  pdb=" N   ARG A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 320
      removed outlier: 3.506A  pdb=" N   ALA A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      Proline residue:  A 299  - end of helix
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 332 through 345
      removed outlier: 4.236A  pdb=" N   VAL A 337 " --> pdb=" O   PRO A 333 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   LEU A 338 " --> pdb=" O   ASP A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 387
      removed outlier: 5.253A  pdb=" N   ARG A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
      Proline residue:  A 385  - end of helix
    Processing helix  chain 'A' and resid 391 through 419
    Processing helix  chain 'A' and resid 422 through 448
      removed outlier: 3.927A  pdb=" N   GLY A 432 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 3.789A  pdb=" N   PHE A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 476
    Processing helix  chain 'A' and resid 519 through 524
    Processing helix  chain 'A' and resid 526 through 528
      No H-bonds generated for 'chain 'A' and resid 526 through 528'
    Processing helix  chain 'A' and resid 529 through 549
    Processing helix  chain 'A' and resid 558 through 562

    303 hydrogen bonds defined for protein.
    888 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: 0.73

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1153
        1.34 -     1.46: 985
        1.46 -     1.58: 1822
        1.58 -     1.70: 0
        1.70 -     1.82: 51
  Bond restraints: 4011
  Sorted by residual:
  bond pdb=" C   ILE A 118 "
       pdb=" N   PRO A 119 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.30e-02 5.92e+03 2.49e+00
  bond pdb=" CB  ILE A 367 "
       pdb=" CG2 ILE A 367 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.47e+00
  bond pdb=" CB  TRP A 529 "
       pdb=" CG  TRP A 529 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.15e+00
  bond pdb=" CB  PRO A 119 "
       pdb=" CG  PRO A 119 "
    ideal  model  delta    sigma   weight residual
    1.492  1.421  0.071 5.00e-02 4.00e+02 2.03e+00
  bond pdb=" CB  PHE A  79 "
       pdb=" CG  PHE A  79 "
    ideal  model  delta    sigma   weight residual
    1.502  1.472  0.030 2.30e-02 1.89e+03 1.73e+00
  ... (remaining 4006 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 5118
        1.75 -     3.49: 274
        3.49 -     5.24: 49
        5.24 -     6.99: 14
        6.99 -     8.73: 7
  Bond angle restraints: 5462
  Sorted by residual:
  angle pdb=" CA  TYR A 190 "
        pdb=" CB  TYR A 190 "
        pdb=" CG  TYR A 190 "
      ideal   model   delta    sigma   weight residual
     113.90  121.31   -7.41 1.80e+00 3.09e-01 1.69e+01
  angle pdb=" C   PHE A 447 "
        pdb=" N   PHE A 448 "
        pdb=" CA  PHE A 448 "
      ideal   model   delta    sigma   weight residual
     122.48  115.90    6.58 1.77e+00 3.19e-01 1.38e+01
  angle pdb=" N   PRO A 453 "
        pdb=" CA  PRO A 453 "
        pdb=" C   PRO A 453 "
      ideal   model   delta    sigma   weight residual
     110.70  114.72   -4.02 1.22e+00 6.72e-01 1.09e+01
  angle pdb=" C   VAL A 189 "
        pdb=" N   TYR A 190 "
        pdb=" CA  TYR A 190 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.07e+01
  angle pdb=" CA  PRO A 453 "
        pdb=" C   PRO A 453 "
        pdb=" N   PRO A 454 "
      ideal   model   delta    sigma   weight residual
     117.93  121.73   -3.80 1.20e+00 6.94e-01 1.00e+01
  ... (remaining 5457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.41: 2174
       14.41 -    28.82: 105
       28.82 -    43.23: 11
       43.23 -    57.64: 3
       57.64 -    72.05: 1
  Dihedral angle restraints: 2294
    sinusoidal: 848
      harmonic: 1446
  Sorted by residual:
  dihedral pdb=" CA  LYS A 224 "
           pdb=" C   LYS A 224 "
           pdb=" N   VAL A 225 "
           pdb=" CA  VAL A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.97   24.03     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 104 "
           pdb=" C   CYS A 104 "
           pdb=" N   CYS A 105 "
           pdb=" CA  CYS A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.82   23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  HIS A 125 "
           pdb=" C   HIS A 125 "
           pdb=" N   LEU A 126 "
           pdb=" CA  LEU A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.06  -20.94     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 2291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 366
       0.038 -    0.076: 167
       0.076 -    0.114: 72
       0.114 -    0.152: 28
       0.152 -    0.190: 3
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" CG  LEU A  35 "
            pdb=" CB  LEU A  35 "
            pdb=" CD1 LEU A  35 "
            pdb=" CD2 LEU A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.00e-01
  chirality pdb=" CB  ILE A 155 "
            pdb=" CA  ILE A 155 "
            pdb=" CG1 ILE A 155 "
            pdb=" CG2 ILE A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CA  TYR A 190 "
            pdb=" N   TYR A 190 "
            pdb=" C   TYR A 190 "
            pdb=" CB  TYR A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.40e-01
  ... (remaining 633 not shown)

  Planarity restraints: 668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 566 "    0.049 5.00e-02 4.00e+02   7.40e-02 8.77e+00
        pdb=" N   PRO A 567 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 567 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 567 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 384 "   -0.042 5.00e-02 4.00e+02   6.30e-02 6.34e+00
        pdb=" N   PRO A 385 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 385 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 385 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 322 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 323 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 323 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 323 "    0.030 5.00e-02 4.00e+02
  ... (remaining 665 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 383
        2.74 -     3.28: 4116
        3.28 -     3.82: 6827
        3.82 -     4.36: 7911
        4.36 -     4.90: 13063
  Nonbonded interactions: 32300
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 122 "
            pdb=" O   ARG A 285 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   MET A 266 "
            pdb=" OG  SER A 269 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER A  74 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ASP A 203 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OE1 GLU A 134 "
            pdb=" NH1 ARG A 142 "
     model   vdw
     2.304 3.120
  ... (remaining 32295 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.060
  Find NCS groups from input model:        0.030
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
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   0.071   4011  Z= 0.294
  Angle     :  0.972   8.733   5462  Z= 0.533
  Chirality :  0.053   0.190    636
  Planarity :  0.009   0.074    668
  Dihedral  :  9.192  72.049   1378
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.30), residues: 504
  helix: -1.71 (0.20), residues: 389
  sheet:  None (None), residues: 0
  loop : -2.13 (0.55), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 384 
 TYR   0.025   0.004   TYR A 190 
 PHE   0.030   0.003   PHE A 468 
 TRP   0.024   0.003   TRP A 469 
 HIS   0.007   0.002   HIS A 254 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00636 /  0.29 ( 4011)
  covalent geometry    : angle       0.97185 /  0.53 ( 5462)
  hydrogen bonds       : bond        0.11707 /  7.95 (  303)
  hydrogen bonds       : angle       7.36806 /  5.13 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8116 (mt) cc_final: 0.7862 (tt)
REVERT: A   61 MET cc_start: 0.9025 (mmm) cc_final: 0.8441 (mmm)
REVERT: A   78 THR cc_start: 0.9180 (m) cc_final: 0.8910 (m)
REVERT: A   94 ARG cc_start: 0.9084 (mtp180) cc_final: 0.8569 (mtp180)
REVERT: A  104 CYS cc_start: 0.7212 (m) cc_final: 0.6955 (t)
REVERT: A  108 LEU cc_start: 0.9165 (mt) cc_final: 0.8932 (mm)
REVERT: A  116 ILE cc_start: 0.8743 (mt) cc_final: 0.8303 (mt)
REVERT: A  120 VAL cc_start: 0.9524 (t) cc_final: 0.9248 (t)
REVERT: A  136 ARG cc_start: 0.9386 (tpt90) cc_final: 0.9094 (tpt90)
REVERT: A  139 LYS cc_start: 0.8752 (tttt) cc_final: 0.8433 (tttt)
REVERT: A  144 CYS cc_start: 0.8982 (m) cc_final: 0.8728 (m)
REVERT: A  152 GLN cc_start: 0.8926 (tt0) cc_final: 0.8552 (tt0)
REVERT: A  166 LEU cc_start: 0.9153 (tp) cc_final: 0.8933 (tp)
REVERT: A  241 ILE cc_start: 0.8842 (mm) cc_final: 0.8531 (mm)
REVERT: A  245 GLU cc_start: 0.8630 (tp30) cc_final: 0.8422 (tp30)
REVERT: A  247 ASP cc_start: 0.8866 (t0) cc_final: 0.8254 (t0)
REVERT: A  249 ASP cc_start: 0.8643 (t0) cc_final: 0.8301 (t0)
REVERT: A  251 PHE cc_start: 0.9098 (m-80) cc_final: 0.8840 (m-10)
REVERT: A  274 ASN cc_start: 0.9074 (t0) cc_final: 0.8580 (t0)
REVERT: A  319 TYR cc_start: 0.8950 (m-80) cc_final: 0.8380 (m-80)
REVERT: A  324 MET cc_start: 0.8211 (ptt) cc_final: 0.7891 (ptm)
REVERT: A  326 ILE cc_start: 0.8871 (mt) cc_final: 0.8177 (mm)
REVERT: A  328 GLN cc_start: 0.8392 (mt0) cc_final: 0.8087 (mm-40)
REVERT: A  338 LEU cc_start: 0.9446 (tp) cc_final: 0.9237 (tp)
REVERT: A  356 ILE cc_start: 0.9094 (mm) cc_final: 0.8571 (tp)
REVERT: A  360 PHE cc_start: 0.8796 (m-80) cc_final: 0.8453 (m-80)
REVERT: A  371 PHE cc_start: 0.9020 (m-10) cc_final: 0.8474 (m-80)
REVERT: A  372 ASN cc_start: 0.9386 (t0) cc_final: 0.9042 (t0)
REVERT: A  400 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7616 (mmm160)
REVERT: A  433 MET cc_start: 0.8630 (mtm) cc_final: 0.8149 (ttm)
REVERT: A  470 ILE cc_start: 0.9013 (mt) cc_final: 0.8705 (mt)
REVERT: A  519 LEU cc_start: 0.8587 (mt) cc_final: 0.7834 (mt)
REVERT: A  520 GLN cc_start: 0.8010 (mt0) cc_final: 0.7686 (mt0)
REVERT: A  530 TYR cc_start: 0.8638 (m-10) cc_final: 0.8359 (m-10)
REVERT: A  558 ASN cc_start: 0.9442 (t0) cc_final: 0.8976 (t0)
REVERT: A  561 THR cc_start: 0.9445 (p) cc_final: 0.9081 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0568
  time to fit residues: 16.7216
Evaluate side-chains
  197 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 214 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112608 restraints weight = 7558.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117399 restraints weight = 4575.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120962 restraints weight = 3109.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.123527 restraints weight = 2275.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125540 restraints weight = 1765.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4011  Z= 0.184
  Angle     :  0.672   7.356   5462  Z= 0.353
  Chirality :  0.042   0.134    636
  Planarity :  0.006   0.047    668
  Dihedral  :  5.731  18.937    549
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.36), residues: 504
  helix: -0.03 (0.24), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.84 (0.62), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 230 
 TYR   0.025   0.002   TYR A 190 
 PHE   0.013   0.002   PHE A 522 
 TRP   0.021   0.002   TRP A 469 
 HIS   0.004   0.002   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.18 ( 4011)
  covalent geometry    : angle       0.67202 /  0.35 ( 5462)
  hydrogen bonds       : bond        0.04390 /  2.88 (  303)
  hydrogen bonds       : angle       5.45000 /  3.80 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8994 (mmm) cc_final: 0.8482 (mmm)
REVERT: A   94 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8725 (mtp180)
REVERT: A  104 CYS cc_start: 0.7085 (m) cc_final: 0.6877 (t)
REVERT: A  139 LYS cc_start: 0.8791 (tttt) cc_final: 0.8456 (tttt)
REVERT: A  142 ARG cc_start: 0.8756 (ttt180) cc_final: 0.7526 (ttt180)
REVERT: A  161 LEU cc_start: 0.9330 (tp) cc_final: 0.9049 (tp)
REVERT: A  242 SER cc_start: 0.9033 (m) cc_final: 0.8695 (p)
REVERT: A  245 GLU cc_start: 0.8618 (tp30) cc_final: 0.8372 (tp30)
REVERT: A  247 ASP cc_start: 0.8661 (t0) cc_final: 0.8212 (t0)
REVERT: A  249 ASP cc_start: 0.8661 (t0) cc_final: 0.8281 (t0)
REVERT: A  251 PHE cc_start: 0.8969 (m-80) cc_final: 0.8756 (m-80)
REVERT: A  255 THR cc_start: 0.8985 (p) cc_final: 0.8630 (p)
REVERT: A  274 ASN cc_start: 0.9109 (t0) cc_final: 0.8672 (t0)
REVERT: A  280 ARG cc_start: 0.9272 (mtt90) cc_final: 0.8867 (mtt180)
REVERT: A  324 MET cc_start: 0.8179 (ptt) cc_final: 0.7771 (ptp)
REVERT: A  330 GLN cc_start: 0.9079 (mt0) cc_final: 0.8878 (mt0)
REVERT: A  356 ILE cc_start: 0.9129 (mm) cc_final: 0.8522 (tp)
REVERT: A  367 ILE cc_start: 0.9317 (mt) cc_final: 0.9083 (mt)
REVERT: A  371 PHE cc_start: 0.9057 (m-10) cc_final: 0.8653 (m-80)
REVERT: A  376 THR cc_start: 0.9518 (m) cc_final: 0.9313 (p)
REVERT: A  397 MET cc_start: 0.8517 (ttp) cc_final: 0.7508 (tmm)
REVERT: A  400 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7330 (mtt180)
REVERT: A  433 MET cc_start: 0.8430 (mtm) cc_final: 0.8073 (ttm)
REVERT: A  519 LEU cc_start: 0.8493 (mt) cc_final: 0.8096 (mt)
REVERT: A  530 TYR cc_start: 0.8625 (m-10) cc_final: 0.8366 (m-10)
REVERT: A  531 SER cc_start: 0.8754 (m) cc_final: 0.8320 (p)
REVERT: A  533 HIS cc_start: 0.8464 (t70) cc_final: 0.8089 (t-90)
REVERT: A  558 ASN cc_start: 0.9573 (t0) cc_final: 0.9188 (t0)
REVERT: A  561 THR cc_start: 0.9367 (p) cc_final: 0.8774 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.0544
  time to fit residues: 15.2900
Evaluate side-chains
  191 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 372 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.143316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.115850 restraints weight = 7637.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.120851 restraints weight = 4666.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124576 restraints weight = 3205.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.127449 restraints weight = 2370.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129579 restraints weight = 1826.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4011  Z= 0.133
  Angle     :  0.621   7.089   5462  Z= 0.318
  Chirality :  0.041   0.151    636
  Planarity :  0.005   0.047    668
  Dihedral  :  5.166  18.398    549
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.38), residues: 504
  helix:  0.71 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.63 (0.64), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.026   0.002   TYR A 523 
 PHE   0.028   0.002   PHE A 360 
 TRP   0.015   0.001   TRP A 177 
 HIS   0.004   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 4011)
  covalent geometry    : angle       0.62123 /  0.32 ( 5462)
  hydrogen bonds       : bond        0.04194 /  2.82 (  303)
  hydrogen bonds       : angle       5.04989 /  3.55 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.9203 (mtp180) cc_final: 0.8806 (mtp180)
REVERT: A  142 ARG cc_start: 0.8658 (ttt180) cc_final: 0.7637 (ttt180)
REVERT: A  151 PHE cc_start: 0.8666 (t80) cc_final: 0.8184 (t80)
REVERT: A  247 ASP cc_start: 0.8589 (t0) cc_final: 0.8144 (t0)
REVERT: A  249 ASP cc_start: 0.8658 (t0) cc_final: 0.8315 (t0)
REVERT: A  255 THR cc_start: 0.8823 (p) cc_final: 0.8373 (p)
REVERT: A  274 ASN cc_start: 0.8751 (t0) cc_final: 0.8401 (t0)
REVERT: A  280 ARG cc_start: 0.9197 (mtt90) cc_final: 0.8631 (mtt180)
REVERT: A  294 CYS cc_start: 0.9434 (t) cc_final: 0.8864 (t)
REVERT: A  319 TYR cc_start: 0.8519 (m-80) cc_final: 0.8259 (m-80)
REVERT: A  324 MET cc_start: 0.7822 (ptt) cc_final: 0.7575 (ptp)
REVERT: A  330 GLN cc_start: 0.8991 (mt0) cc_final: 0.8745 (mt0)
REVERT: A  360 PHE cc_start: 0.8632 (m-80) cc_final: 0.8398 (m-80)
REVERT: A  367 ILE cc_start: 0.9317 (mt) cc_final: 0.9053 (mt)
REVERT: A  371 PHE cc_start: 0.9041 (m-10) cc_final: 0.8565 (m-10)
REVERT: A  376 THR cc_start: 0.9493 (m) cc_final: 0.9278 (p)
REVERT: A  397 MET cc_start: 0.8446 (ttp) cc_final: 0.7510 (tmm)
REVERT: A  433 MET cc_start: 0.8320 (mtm) cc_final: 0.7897 (ttm)
REVERT: A  442 PHE cc_start: 0.8495 (m-10) cc_final: 0.8286 (m-10)
REVERT: A  527 TYR cc_start: 0.9228 (p90) cc_final: 0.8913 (p90)
REVERT: A  529 TRP cc_start: 0.8832 (m100) cc_final: 0.8628 (m100)
REVERT: A  530 TYR cc_start: 0.8651 (m-10) cc_final: 0.8352 (m-10)
REVERT: A  531 SER cc_start: 0.8731 (m) cc_final: 0.8214 (p)
REVERT: A  533 HIS cc_start: 0.8471 (t70) cc_final: 0.7995 (t-90)
REVERT: A  557 LEU cc_start: 0.8501 (tp) cc_final: 0.8103 (mt)
REVERT: A  558 ASN cc_start: 0.9565 (t0) cc_final: 0.9204 (t0)
REVERT: A  561 THR cc_start: 0.9240 (p) cc_final: 0.8678 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0435
  time to fit residues: 12.1051
Evaluate side-chains
  180 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 335 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.116000 restraints weight = 7860.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.120930 restraints weight = 4881.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.124640 restraints weight = 3384.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.127340 restraints weight = 2515.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.129525 restraints weight = 1973.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4011  Z= 0.138
  Angle     :  0.608   6.638   5462  Z= 0.310
  Chirality :  0.040   0.131    636
  Planarity :  0.005   0.052    668
  Dihedral  :  4.943  20.111    549
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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 are not related in a simple way.
  whole:  0.74 (0.38), residues: 504
  helix:  0.97 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.34 (0.65), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.025   0.002   TYR A 339 
 PHE   0.021   0.002   PHE A 360 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.14 ( 4011)
  covalent geometry    : angle       0.60781 /  0.31 ( 5462)
  hydrogen bonds       : bond        0.03884 /  2.57 (  303)
  hydrogen bonds       : angle       4.81204 /  3.39 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9084 (mmm) cc_final: 0.8462 (mmm)
REVERT: A   94 ARG cc_start: 0.9199 (mtp180) cc_final: 0.8825 (mtp180)
REVERT: A  142 ARG cc_start: 0.8757 (ttt180) cc_final: 0.7569 (ttt180)
REVERT: A  157 MET cc_start: 0.8371 (mtm) cc_final: 0.8028 (mtm)
REVERT: A  242 SER cc_start: 0.8997 (m) cc_final: 0.8732 (p)
REVERT: A  247 ASP cc_start: 0.8559 (t0) cc_final: 0.8180 (t0)
REVERT: A  249 ASP cc_start: 0.8679 (t0) cc_final: 0.8375 (t0)
REVERT: A  255 THR cc_start: 0.8782 (p) cc_final: 0.8298 (p)
REVERT: A  274 ASN cc_start: 0.8942 (t0) cc_final: 0.8418 (t0)
REVERT: A  280 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8668 (mtt180)
REVERT: A  301 GLN cc_start: 0.8425 (tp40) cc_final: 0.7933 (tm-30)
REVERT: A  326 ILE cc_start: 0.8830 (mm) cc_final: 0.8625 (mm)
REVERT: A  330 GLN cc_start: 0.8944 (mt0) cc_final: 0.8627 (mt0)
REVERT: A  335 GLN cc_start: 0.8491 (pt0) cc_final: 0.8189 (pm20)
REVERT: A  338 LEU cc_start: 0.9490 (tp) cc_final: 0.9277 (tp)
REVERT: A  356 ILE cc_start: 0.8892 (mt) cc_final: 0.8231 (mt)
REVERT: A  360 PHE cc_start: 0.8649 (m-80) cc_final: 0.8429 (m-80)
REVERT: A  367 ILE cc_start: 0.9312 (mt) cc_final: 0.9109 (mt)
REVERT: A  371 PHE cc_start: 0.8995 (m-10) cc_final: 0.8585 (m-10)
REVERT: A  376 THR cc_start: 0.9474 (m) cc_final: 0.9269 (p)
REVERT: A  397 MET cc_start: 0.8416 (ttp) cc_final: 0.7455 (tmm)
REVERT: A  433 MET cc_start: 0.8352 (mtm) cc_final: 0.7849 (ttm)
REVERT: A  530 TYR cc_start: 0.8677 (m-10) cc_final: 0.8443 (m-10)
REVERT: A  531 SER cc_start: 0.8758 (m) cc_final: 0.8200 (p)
REVERT: A  533 HIS cc_start: 0.8502 (t70) cc_final: 0.8022 (t-90)
REVERT: A  558 ASN cc_start: 0.9540 (t0) cc_final: 0.9173 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0528
  time to fit residues: 13.5293
Evaluate side-chains
  179 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.141263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114151 restraints weight = 7767.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118979 restraints weight = 4856.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122653 restraints weight = 3373.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.125199 restraints weight = 2497.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.127321 restraints weight = 1955.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4011  Z= 0.175
  Angle     :  0.663   7.191   5462  Z= 0.337
  Chirality :  0.042   0.154    636
  Planarity :  0.005   0.047    668
  Dihedral  :  4.852  16.713    549
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.38), residues: 504
  helix:  0.98 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.24 (0.65), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.024   0.002   TYR A 156 
 PHE   0.020   0.002   PHE A 360 
 TRP   0.016   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.17 ( 4011)
  covalent geometry    : angle       0.66288 /  0.34 ( 5462)
  hydrogen bonds       : bond        0.04071 /  2.71 (  303)
  hydrogen bonds       : angle       4.90324 /  3.45 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9050 (mmm) cc_final: 0.8582 (mmm)
REVERT: A   94 ARG cc_start: 0.9206 (mtp180) cc_final: 0.8706 (mtp180)
REVERT: A  142 ARG cc_start: 0.8780 (ttt180) cc_final: 0.7665 (ttt180)
REVERT: A  242 SER cc_start: 0.8998 (m) cc_final: 0.8701 (p)
REVERT: A  247 ASP cc_start: 0.8684 (t0) cc_final: 0.8261 (t0)
REVERT: A  249 ASP cc_start: 0.8655 (t0) cc_final: 0.8298 (t0)
REVERT: A  251 PHE cc_start: 0.8873 (m-80) cc_final: 0.8659 (m-80)
REVERT: A  255 THR cc_start: 0.8735 (p) cc_final: 0.8258 (p)
REVERT: A  274 ASN cc_start: 0.9040 (t0) cc_final: 0.8307 (t0)
REVERT: A  301 GLN cc_start: 0.8538 (tp40) cc_final: 0.8227 (tt0)
REVERT: A  319 TYR cc_start: 0.8137 (m-80) cc_final: 0.7860 (m-80)
REVERT: A  326 ILE cc_start: 0.8771 (mm) cc_final: 0.8418 (mm)
REVERT: A  330 GLN cc_start: 0.9090 (mt0) cc_final: 0.8736 (mt0)
REVERT: A  335 GLN cc_start: 0.8565 (pt0) cc_final: 0.8267 (pm20)
REVERT: A  338 LEU cc_start: 0.9502 (tp) cc_final: 0.9233 (tp)
REVERT: A  356 ILE cc_start: 0.8881 (mt) cc_final: 0.7738 (tp)
REVERT: A  360 PHE cc_start: 0.8696 (m-80) cc_final: 0.8347 (m-80)
REVERT: A  374 LEU cc_start: 0.9076 (mt) cc_final: 0.8828 (mt)
REVERT: A  397 MET cc_start: 0.8439 (ttp) cc_final: 0.7474 (tmm)
REVERT: A  433 MET cc_start: 0.8460 (mtm) cc_final: 0.7840 (ttm)
REVERT: A  531 SER cc_start: 0.8848 (m) cc_final: 0.8262 (p)
REVERT: A  533 HIS cc_start: 0.8581 (t70) cc_final: 0.8155 (t-90)
REVERT: A  558 ASN cc_start: 0.9522 (t0) cc_final: 0.9228 (t0)
REVERT: A  561 THR cc_start: 0.9302 (p) cc_final: 0.8834 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0506
  time to fit residues: 13.2979
Evaluate side-chains
  179 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 HIS
A 335 GLN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.145096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.117442 restraints weight = 7741.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.122480 restraints weight = 4870.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.126191 restraints weight = 3374.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.128886 restraints weight = 2491.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.130621 restraints weight = 1941.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4011  Z= 0.132
  Angle     :  0.619   6.981   5462  Z= 0.310
  Chirality :  0.040   0.143    636
  Planarity :  0.004   0.043    668
  Dihedral  :  4.678  15.572    549
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.39), residues: 504
  helix:  1.13 (0.26), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.13 (0.67), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.020   0.002   TYR A 156 
 PHE   0.025   0.002   PHE A 360 
 TRP   0.012   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 ( 4011)
  covalent geometry    : angle       0.61878 /  0.31 ( 5462)
  hydrogen bonds       : bond        0.03887 /  2.58 (  303)
  hydrogen bonds       : angle       4.74966 /  3.35 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8690 (mtp180)
REVERT: A  142 ARG cc_start: 0.8707 (ttt180) cc_final: 0.7640 (ttt180)
REVERT: A  242 SER cc_start: 0.9018 (m) cc_final: 0.8796 (p)
REVERT: A  247 ASP cc_start: 0.8625 (t0) cc_final: 0.8203 (t0)
REVERT: A  249 ASP cc_start: 0.8739 (t0) cc_final: 0.8360 (t0)
REVERT: A  274 ASN cc_start: 0.8988 (t0) cc_final: 0.8239 (t0)
REVERT: A  275 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8197 (mm110)
REVERT: A  324 MET cc_start: 0.7164 (ptm) cc_final: 0.6938 (ttp)
REVERT: A  335 GLN cc_start: 0.8537 (pt0) cc_final: 0.8260 (pm20)
REVERT: A  338 LEU cc_start: 0.9455 (tp) cc_final: 0.9246 (tp)
REVERT: A  356 ILE cc_start: 0.8862 (mt) cc_final: 0.7689 (tp)
REVERT: A  360 PHE cc_start: 0.8593 (m-80) cc_final: 0.8241 (m-80)
REVERT: A  372 ASN cc_start: 0.9242 (t0) cc_final: 0.8814 (t0)
REVERT: A  397 MET cc_start: 0.8384 (ttp) cc_final: 0.7366 (tmm)
REVERT: A  433 MET cc_start: 0.8381 (mtm) cc_final: 0.7791 (ttm)
REVERT: A  452 ASN cc_start: 0.7840 (t0) cc_final: 0.6964 (m-40)
REVERT: A  531 SER cc_start: 0.8838 (m) cc_final: 0.8246 (p)
REVERT: A  533 HIS cc_start: 0.8528 (t70) cc_final: 0.8115 (t-90)
REVERT: A  558 ASN cc_start: 0.9598 (t0) cc_final: 0.9253 (t0)
REVERT: A  561 THR cc_start: 0.9303 (p) cc_final: 0.8862 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0490
  time to fit residues: 12.8136
Evaluate side-chains
  174 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117027 restraints weight = 7876.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.121902 restraints weight = 4995.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125634 restraints weight = 3490.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.128396 restraints weight = 2610.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.130351 restraints weight = 2046.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4011  Z= 0.134
  Angle     :  0.632   7.494   5462  Z= 0.320
  Chirality :  0.040   0.135    636
  Planarity :  0.005   0.044    668
  Dihedral  :  4.556  15.338    549
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.38), residues: 504
  helix:  0.99 (0.26), residues: 415
  sheet:  None (None), residues: 0
  loop : -1.46 (0.66), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.037   0.002   TYR A 190 
 PHE   0.035   0.002   PHE A 371 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 4011)
  covalent geometry    : angle       0.63240 /  0.32 ( 5462)
  hydrogen bonds       : bond        0.03956 /  2.61 (  303)
  hydrogen bonds       : angle       4.79653 /  3.38 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8948 (mmm) cc_final: 0.8241 (mmm)
REVERT: A   94 ARG cc_start: 0.9179 (mtp180) cc_final: 0.8716 (mtp180)
REVERT: A  142 ARG cc_start: 0.8693 (ttt180) cc_final: 0.7646 (ttt180)
REVERT: A  242 SER cc_start: 0.9005 (m) cc_final: 0.8804 (p)
REVERT: A  247 ASP cc_start: 0.8591 (t0) cc_final: 0.8146 (t0)
REVERT: A  249 ASP cc_start: 0.8712 (t0) cc_final: 0.8319 (t0)
REVERT: A  274 ASN cc_start: 0.9016 (t0) cc_final: 0.8371 (t0)
REVERT: A  275 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8193 (mm110)
REVERT: A  319 TYR cc_start: 0.8603 (m-80) cc_final: 0.8178 (m-10)
REVERT: A  335 GLN cc_start: 0.8507 (pt0) cc_final: 0.8260 (pm20)
REVERT: A  338 LEU cc_start: 0.9459 (tp) cc_final: 0.9249 (tp)
REVERT: A  356 ILE cc_start: 0.8902 (mt) cc_final: 0.7664 (tp)
REVERT: A  360 PHE cc_start: 0.8609 (m-80) cc_final: 0.8277 (m-80)
REVERT: A  372 ASN cc_start: 0.9189 (t0) cc_final: 0.8758 (t0)
REVERT: A  397 MET cc_start: 0.8385 (ttp) cc_final: 0.7363 (tmm)
REVERT: A  433 MET cc_start: 0.8400 (mtm) cc_final: 0.7677 (ttm)
REVERT: A  531 SER cc_start: 0.8857 (m) cc_final: 0.8227 (p)
REVERT: A  533 HIS cc_start: 0.8536 (t70) cc_final: 0.8067 (t-90)
REVERT: A  561 THR cc_start: 0.9279 (p) cc_final: 0.8950 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0511
  time to fit residues: 12.7544
Evaluate side-chains
  173 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.118152 restraints weight = 7667.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123061 restraints weight = 4940.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126837 restraints weight = 3467.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.129647 restraints weight = 2591.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.131889 restraints weight = 2037.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4011  Z= 0.133
  Angle     :  0.643   7.750   5462  Z= 0.323
  Chirality :  0.040   0.163    636
  Planarity :  0.005   0.053    668
  Dihedral  :  4.488  16.024    549
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.38), residues: 504
  helix:  0.95 (0.26), residues: 417
  sheet:  None (None), residues: 0
  loop : -1.27 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.035   0.002   TYR A 190 
 PHE   0.027   0.002   PHE A 371 
 TRP   0.014   0.001   TRP A 232 
 HIS   0.003   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 4011)
  covalent geometry    : angle       0.64295 /  0.32 ( 5462)
  hydrogen bonds       : bond        0.03905 /  2.60 (  303)
  hydrogen bonds       : angle       4.69555 /  3.27 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8900 (mmm) cc_final: 0.8198 (mmm)
REVERT: A   94 ARG cc_start: 0.9186 (mtp180) cc_final: 0.8717 (mtp180)
REVERT: A  142 ARG cc_start: 0.8681 (ttt180) cc_final: 0.7611 (ttt180)
REVERT: A  224 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7128 (tmtt)
REVERT: A  242 SER cc_start: 0.8997 (m) cc_final: 0.8784 (p)
REVERT: A  247 ASP cc_start: 0.8573 (t0) cc_final: 0.8123 (t0)
REVERT: A  249 ASP cc_start: 0.8686 (t0) cc_final: 0.8262 (t0)
REVERT: A  274 ASN cc_start: 0.8968 (t0) cc_final: 0.8322 (t0)
REVERT: A  275 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8190 (mm110)
REVERT: A  319 TYR cc_start: 0.8632 (m-80) cc_final: 0.8201 (m-10)
REVERT: A  335 GLN cc_start: 0.8541 (pt0) cc_final: 0.8296 (pm20)
REVERT: A  338 LEU cc_start: 0.9479 (tp) cc_final: 0.9267 (tp)
REVERT: A  356 ILE cc_start: 0.8883 (mt) cc_final: 0.7591 (tp)
REVERT: A  360 PHE cc_start: 0.8636 (m-80) cc_final: 0.8311 (m-80)
REVERT: A  372 ASN cc_start: 0.9270 (t0) cc_final: 0.8872 (t0)
REVERT: A  397 MET cc_start: 0.8367 (ttp) cc_final: 0.7299 (tmm)
REVERT: A  433 MET cc_start: 0.8334 (mtm) cc_final: 0.7609 (ttm)
REVERT: A  531 SER cc_start: 0.8868 (m) cc_final: 0.8230 (p)
REVERT: A  533 HIS cc_start: 0.8475 (t70) cc_final: 0.8000 (t-90)
REVERT: A  561 THR cc_start: 0.9235 (p) cc_final: 0.8942 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0427
  time to fit residues: 10.7156
Evaluate side-chains
  174 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.117190 restraints weight = 7812.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122151 restraints weight = 4965.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.125862 restraints weight = 3480.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128716 restraints weight = 2587.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.130695 restraints weight = 2022.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4011  Z= 0.135
  Angle     :  0.647   8.775   5462  Z= 0.329
  Chirality :  0.041   0.185    636
  Planarity :  0.004   0.041    668
  Dihedral  :  4.418  14.725    549
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.38), residues: 504
  helix:  1.02 (0.26), residues: 418
  sheet:  None (None), residues: 0
  loop : -1.11 (0.69), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 230 
 TYR   0.016   0.002   TYR A 523 
 PHE   0.023   0.002   PHE A 371 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 4011)
  covalent geometry    : angle       0.64654 /  0.33 ( 5462)
  hydrogen bonds       : bond        0.03886 /  2.61 (  303)
  hydrogen bonds       : angle       4.68441 /  3.27 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8821 (mmm) cc_final: 0.8270 (mmm)
REVERT: A   94 ARG cc_start: 0.9181 (mtp180) cc_final: 0.8714 (mtp180)
REVERT: A  142 ARG cc_start: 0.8668 (ttt180) cc_final: 0.7609 (ttt180)
REVERT: A  206 GLN cc_start: 0.8892 (mp10) cc_final: 0.8609 (mp10)
REVERT: A  242 SER cc_start: 0.8989 (m) cc_final: 0.8785 (p)
REVERT: A  247 ASP cc_start: 0.8588 (t0) cc_final: 0.8119 (t0)
REVERT: A  249 ASP cc_start: 0.8656 (t0) cc_final: 0.8215 (t0)
REVERT: A  258 THR cc_start: 0.9079 (m) cc_final: 0.8644 (m)
REVERT: A  274 ASN cc_start: 0.9001 (t0) cc_final: 0.8395 (t0)
REVERT: A  275 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7535 (mm110)
REVERT: A  319 TYR cc_start: 0.8652 (m-80) cc_final: 0.8205 (m-10)
REVERT: A  335 GLN cc_start: 0.8506 (pt0) cc_final: 0.8259 (pm20)
REVERT: A  338 LEU cc_start: 0.9485 (tp) cc_final: 0.9281 (tp)
REVERT: A  356 ILE cc_start: 0.8872 (mt) cc_final: 0.7542 (tp)
REVERT: A  360 PHE cc_start: 0.8710 (m-80) cc_final: 0.8431 (m-80)
REVERT: A  372 ASN cc_start: 0.9285 (t0) cc_final: 0.8887 (t0)
REVERT: A  397 MET cc_start: 0.8358 (ttp) cc_final: 0.7297 (tmm)
REVERT: A  433 MET cc_start: 0.8244 (mtm) cc_final: 0.7586 (ttm)
REVERT: A  529 TRP cc_start: 0.8928 (m100) cc_final: 0.8336 (m100)
REVERT: A  533 HIS cc_start: 0.8444 (t70) cc_final: 0.8058 (t70)
REVERT: A  561 THR cc_start: 0.9169 (p) cc_final: 0.8906 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0432
  time to fit residues: 10.8473
Evaluate side-chains
  171 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.147028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.117021 restraints weight = 7818.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.122005 restraints weight = 5078.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.125554 restraints weight = 3620.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.128296 restraints weight = 2771.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.130536 restraints weight = 2227.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4011  Z= 0.134
  Angle     :  0.636   7.891   5462  Z= 0.322
  Chirality :  0.041   0.153    636
  Planarity :  0.005   0.049    668
  Dihedral  :  4.419  14.802    549
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.38), residues: 504
  helix:  1.03 (0.26), residues: 417
  sheet:  None (None), residues: 0
  loop : -1.20 (0.69), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 230 
 TYR   0.016   0.002   TYR A 523 
 PHE   0.024   0.002   PHE A 371 
 TRP   0.012   0.001   TRP A 469 
 HIS   0.002   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 4011)
  covalent geometry    : angle       0.63648 /  0.32 ( 5462)
  hydrogen bonds       : bond        0.03819 /  2.55 (  303)
  hydrogen bonds       : angle       4.68446 /  3.27 (  888)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8716 (mmm) cc_final: 0.8183 (mmm)
REVERT: A   94 ARG cc_start: 0.9188 (mtp180) cc_final: 0.8727 (mtp180)
REVERT: A  142 ARG cc_start: 0.8676 (ttt180) cc_final: 0.7590 (ttt180)
REVERT: A  206 GLN cc_start: 0.8899 (mp10) cc_final: 0.8478 (mp10)
REVERT: A  242 SER cc_start: 0.8996 (m) cc_final: 0.8785 (p)
REVERT: A  247 ASP cc_start: 0.8579 (t0) cc_final: 0.8114 (t0)
REVERT: A  249 ASP cc_start: 0.8639 (t0) cc_final: 0.8189 (t0)
REVERT: A  258 THR cc_start: 0.9046 (m) cc_final: 0.8635 (m)
REVERT: A  274 ASN cc_start: 0.9010 (t0) cc_final: 0.8386 (t0)
REVERT: A  275 GLN cc_start: 0.8657 (mm-40) cc_final: 0.7923 (mm110)
REVERT: A  335 GLN cc_start: 0.8513 (pt0) cc_final: 0.8271 (pm20)
REVERT: A  356 ILE cc_start: 0.8876 (mt) cc_final: 0.7592 (tp)
REVERT: A  360 PHE cc_start: 0.8752 (m-80) cc_final: 0.8384 (m-80)
REVERT: A  372 ASN cc_start: 0.9318 (t0) cc_final: 0.8937 (t0)
REVERT: A  397 MET cc_start: 0.8350 (ttp) cc_final: 0.7230 (tmm)
REVERT: A  529 TRP cc_start: 0.8917 (m100) cc_final: 0.8265 (m100)
REVERT: A  530 TYR cc_start: 0.8791 (m-10) cc_final: 0.8583 (m-10)
REVERT: A  533 HIS cc_start: 0.8462 (t70) cc_final: 0.8012 (t70)
REVERT: A  561 THR cc_start: 0.9149 (p) cc_final: 0.8886 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0421
  time to fit residues: 10.2225
Evaluate side-chains
  170 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0270
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.147960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118083 restraints weight = 7774.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.123045 restraints weight = 5059.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126786 restraints weight = 3610.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.129657 restraints weight = 2745.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.131743 restraints weight = 2178.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4011  Z= 0.138
  Angle     :  0.707  10.459   5462  Z= 0.351
  Chirality :  0.043   0.274    636
  Planarity :  0.005   0.044    668
  Dihedral  :  4.420  13.958    549
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.38), residues: 504
  helix:  1.08 (0.26), residues: 417
  sheet:  None (None), residues: 0
  loop : -1.09 (0.69), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.024   0.002   TYR A 339 
 PHE   0.025   0.002   PHE A 340 
 TRP   0.012   0.001   TRP A 177 
 HIS   0.002   0.001   HIS A 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 ( 4011)
  covalent geometry    : angle       0.70693 /  0.35 ( 5462)
  hydrogen bonds       : bond        0.03945 /  2.63 (  303)
  hydrogen bonds       : angle       4.68600 /  3.29 (  888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 852.53 seconds
wall clock time: 15 minutes 22.65 seconds (922.65 seconds total)