Starting phenix.real_space_refine
on Tue Feb 11 13:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jc3_9793/02_2025/6jc3_9793.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3154 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      19      5.16       5
     C    1953      2.51       5
     N     545      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3154
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3034
          Classifications: {'peptide': 391}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 378}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 120
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
  Time building chain proxies: 2.48, per 1000 atoms: 0.79
  Number of scatterers: 3154
  At special positions: 0
  Unit cell: (74.25, 87.75, 89.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P       6     15.00
     O     631      8.00
     N     545      7.00
     C    1953      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: 0.76
  Conformation dependent library (CDL) restraints added in 331.8 milliseconds
  

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      67.3% alpha, 0.0% beta
      0 base pairs and 3 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 15
      removed outlier: 4.069A  pdb=" N   ALA A  14 " --> pdb=" O   GLN A  10 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLN A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 60
    Processing helix  chain 'A' and resid 65 through 79
      removed outlier: 3.539A  pdb=" N   ARG A  69 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 93
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.786A  pdb=" N   PHE A 128 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   MET A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
      removed outlier: 3.786A  pdb=" N   VAL A 150 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   GLU A 151 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 147 through 151'
    Processing helix  chain 'A' and resid 157 through 175
      removed outlier: 3.986A  pdb=" N   THR A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 204 through 208
      removed outlier: 3.648A  pdb=" N   TYR A 207 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE A 208 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 208'
    Processing helix  chain 'A' and resid 210 through 224
    Processing helix  chain 'A' and resid 224 through 241
      removed outlier: 4.082A  pdb=" N   ARG A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 260
      removed outlier: 3.525A  pdb=" N   ASN A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   SER A 257 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   TYR A 258 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 287 through 303
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 316 through 323
      removed outlier: 3.922A  pdb=" N   GLN A 319 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 327 through 342
    Processing helix  chain 'A' and resid 356 through 369
      removed outlier: 3.849A  pdb=" N   TRP A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ALA A 369 " --> pdb=" O   GLU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
    Processing helix  chain 'A' and resid 385 through 397

    159 hydrogen bonds defined for protein.
    459 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      3 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 566
        1.32 -     1.45: 863
        1.45 -     1.57: 1740
        1.57 -     1.70: 11
        1.70 -     1.83: 34
  Bond restraints: 3214
  Sorted by residual:
  bond pdb=" CA  MET A 129 "
       pdb=" C   MET A 129 "
    ideal  model  delta    sigma   weight residual
    1.524  1.485  0.039 1.27e-02 6.20e+03 9.42e+00
  bond pdb=" CA  GLU A 184 "
       pdb=" C   GLU A 184 "
    ideal  model  delta    sigma   weight residual
    1.523  1.484  0.039 1.32e-02 5.74e+03 8.65e+00
  bond pdb=" N   THR A 185 "
       pdb=" CA  THR A 185 "
    ideal  model  delta    sigma   weight residual
    1.462  1.425  0.037 1.26e-02 6.30e+03 8.51e+00
  bond pdb=" CA  PHE A 350 "
       pdb=" CB  PHE A 350 "
    ideal  model  delta    sigma   weight residual
    1.535  1.447  0.088 3.03e-02 1.09e+03 8.40e+00
  bond pdb=" N   PHE A 114 "
       pdb=" CA  PHE A 114 "
    ideal  model  delta    sigma   weight residual
    1.462  1.424  0.037 1.35e-02 5.49e+03 7.57e+00
  ... (remaining 3209 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 4201
        2.95 -     5.91: 133
        5.91 -     8.86: 18
        8.86 -    11.81: 11
       11.81 -    14.77: 1
  Bond angle restraints: 4364
  Sorted by residual:
  angle pdb=" N   MET A 129 "
        pdb=" CA  MET A 129 "
        pdb=" C   MET A 129 "
      ideal   model   delta    sigma   weight residual
     111.07   96.30   14.77 1.07e+00 8.73e-01 1.90e+02
  angle pdb=" CA  ARG A 124 "
        pdb=" C   ARG A 124 "
        pdb=" N   ALA A 125 "
      ideal   model   delta    sigma   weight residual
     117.63  106.48   11.15 1.25e+00 6.40e-01 7.95e+01
  angle pdb=" N   LEU A 282 "
        pdb=" CA  LEU A 282 "
        pdb=" C   LEU A 282 "
      ideal   model   delta    sigma   weight residual
     111.28  101.96    9.32 1.09e+00 8.42e-01 7.31e+01
  angle pdb=" N   ARG A 127 "
        pdb=" CA  ARG A 127 "
        pdb=" C   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     111.14  119.82   -8.68 1.08e+00 8.57e-01 6.47e+01
  angle pdb=" N   GLN A 319 "
        pdb=" CA  GLN A 319 "
        pdb=" C   GLN A 319 "
      ideal   model   delta    sigma   weight residual
     111.28  102.76    8.52 1.09e+00 8.42e-01 6.11e+01
  ... (remaining 4359 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.35: 1669
       15.35 -    30.71: 220
       30.71 -    46.06: 55
       46.06 -    61.41: 24
       61.41 -    76.77: 4
  Dihedral angle restraints: 1972
    sinusoidal: 837
      harmonic: 1135
  Sorted by residual:
  dihedral pdb=" CA  ASN A  41 "
           pdb=" C   ASN A  41 "
           pdb=" N   SER A  42 "
           pdb=" CA  SER A  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.72  -24.28     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  LEU A 264 "
           pdb=" C   LEU A 264 "
           pdb=" N   THR A 265 "
           pdb=" CA  THR A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.88  -22.12     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" N   GLN A 113 "
           pdb=" C   GLN A 113 "
           pdb=" CA  GLN A 113 "
           pdb=" CB  GLN A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.67  -10.87     0      2.50e+00 1.60e-01 1.89e+01
  ... (remaining 1969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 439
       0.100 -    0.200: 54
       0.200 -    0.300: 4
       0.300 -    0.400: 1
       0.400 -    0.500: 1
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" CA  GLN A 113 "
            pdb=" N   GLN A 113 "
            pdb=" C   GLN A 113 "
            pdb=" CB  GLN A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.24e+00
  chirality pdb=" CA  PRO A 112 "
            pdb=" N   PRO A 112 "
            pdb=" C   PRO A 112 "
            pdb=" CB  PRO A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  GLN A 319 "
            pdb=" N   GLN A 319 "
            pdb=" C   GLN A 319 "
            pdb=" CB  GLN A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 496 not shown)

  Planarity restraints: 549
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 124 "   -0.024 2.00e-02 2.50e+03   5.14e-02 2.64e+01
        pdb=" C   ARG A 124 "    0.089 2.00e-02 2.50e+03
        pdb=" O   ARG A 124 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   ALA A 125 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 143 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.48e+00
        pdb=" N   PRO A 144 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 144 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 144 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U N  38 "    0.027 2.00e-02 2.50e+03   1.45e-02 4.75e+00
        pdb=" N1    U N  38 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    U N  38 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2    U N  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    U N  38 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    U N  38 "    0.007 2.00e-02 2.50e+03
        pdb=" O4    U N  38 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    U N  38 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    U N  38 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 546 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 11
        2.19 -     2.87: 1312
        2.87 -     3.54: 4378
        3.54 -     4.22: 6957
        4.22 -     4.90: 10890
  Nonbonded interactions: 23548
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 314 "
            pdb=" OD1 ASP A 316 "
     model   vdw
     1.512 3.460
  nonbonded pdb=" NE2 GLN A 319 "
            pdb=" N   MET A 320 "
     model   vdw
     1.625 3.200
  nonbonded pdb=" CE1 PHE A 107 "
            pdb=" CA  PHE A 114 "
     model   vdw
     1.904 3.770
  nonbonded pdb=" O   ASP A 318 "
            pdb=" OG  SER A 321 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" CG  MET A 180 "
            pdb=" OE2 GLU A 184 "
     model   vdw
     2.001 3.440
  ... (remaining 23543 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
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      :  0.010   0.088   3214  Z= 0.693
  Angle     :  1.350  14.766   4364  Z= 0.820
  Chirality :  0.069   0.500    499
  Planarity :  0.008   0.064    549
  Dihedral  : 16.287  76.766   1240
  Min Nonbonded Distance : 1.512

Molprobity Statistics.
  All-atom Clashscore : 30.30
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  : 10.08 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.17 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.39 (0.35), residues: 387
  helix: -3.13 (0.24), residues: 208
  sheet: -2.62 (1.32), residues: 10
  loop : -2.47 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.004   TRP A 173 
 HIS   0.003   0.002   HIS A  87 
 PHE   0.023   0.003   PHE A 145 
 TYR   0.020   0.004   TYR A 249 
 ARG   0.009   0.002   ARG A  69 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8566 (pm20)
REVERT: A  135 LEU cc_start: 0.8057 (mt) cc_final: 0.7491 (mt)
REVERT: A  178 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8874 (mppt)
REVERT: A  184 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.4327 (mt-10)
REVERT: A  256 ASP cc_start: 0.9568 (t70) cc_final: 0.9325 (t0)
REVERT: A  258 TYR cc_start: 0.8391 (m-80) cc_final: 0.8164 (m-80)
REVERT: A  278 LYS cc_start: 0.7222 (mttt) cc_final: 0.6323 (tppt)
REVERT: A  282 LEU cc_start: 0.9301 (tt) cc_final: 0.8883 (mt)
REVERT: A  295 LYS cc_start: 0.6852 (mttt) cc_final: 0.5860 (ptmt)
REVERT: A  311 MET cc_start: 0.9183 (mtt) cc_final: 0.8907 (tpp)
REVERT: A  365 GLU cc_start: 0.8539 (tp30) cc_final: 0.8275 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 138
  average time/residue: 0.2224
  time to fit residues: 35.0767
Evaluate side-chains
  79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0060
   chunk 11 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
A  87 HIS
A 218 GLN
A 296 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.075855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.064296 restraints weight = 14303.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.066335 restraints weight = 8719.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.067780 restraints weight = 5995.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3214  Z= 0.184
  Angle     :  0.647   6.212   4364  Z= 0.336
  Chirality :  0.041   0.165    499
  Planarity :  0.005   0.042    549
  Dihedral  : 10.710  59.064    523
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.88 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.72 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.40), residues: 387
  helix: -0.50 (0.30), residues: 235
  sheet: -2.08 (1.36), residues: 10
  loop : -1.94 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 360 
 HIS   0.002   0.001   HIS A 210 
 PHE   0.016   0.002   PHE A  54 
 TYR   0.005   0.001   TYR A 310 
 ARG   0.006   0.001   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9499 (m-30) cc_final: 0.9109 (m-30)
REVERT: A  103 GLU cc_start: 0.8943 (tt0) cc_final: 0.8371 (pm20)
REVERT: A  130 MET cc_start: 0.9483 (mmp) cc_final: 0.9269 (mmm)
REVERT: A  135 LEU cc_start: 0.7700 (mt) cc_final: 0.7461 (mt)
REVERT: A  173 TRP cc_start: 0.9455 (m100) cc_final: 0.9024 (m100)
REVERT: A  231 LEU cc_start: 0.9546 (mt) cc_final: 0.9282 (mt)
REVERT: A  241 THR cc_start: 0.7251 (m) cc_final: 0.6849 (t)
REVERT: A  256 ASP cc_start: 0.9205 (t70) cc_final: 0.8375 (t70)
REVERT: A  261 ASN cc_start: 0.8091 (m-40) cc_final: 0.7515 (m-40)
REVERT: A  271 LEU cc_start: 0.9021 (mm) cc_final: 0.8382 (mm)
REVERT: A  294 MET cc_start: 0.8510 (mmm) cc_final: 0.8120 (mmt)
REVERT: A  302 ARG cc_start: 0.3146 (mtt-85) cc_final: 0.2820 (ttm170)
REVERT: A  303 MET cc_start: 0.9131 (ppp) cc_final: 0.8870 (ppp)
REVERT: A  355 MET cc_start: 0.8545 (ttt) cc_final: 0.8336 (ttm)
REVERT: A  362 LEU cc_start: 0.9449 (tt) cc_final: 0.8867 (mm)
REVERT: A  365 GLU cc_start: 0.8325 (tp30) cc_final: 0.8043 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1820
  time to fit residues: 18.5088
Evaluate side-chains
  65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 20 optimal weight:    0.3980
   chunk 23 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 GLN
A 296 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.068530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.058260 restraints weight = 15209.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.060026 restraints weight = 9128.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.061182 restraints weight = 6206.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3214  Z= 0.262
  Angle     :  0.665  10.599   4364  Z= 0.349
  Chirality :  0.041   0.165    499
  Planarity :  0.005   0.049    549
  Dihedral  : 10.549  60.841    523
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.42), residues: 387
  helix:  0.61 (0.32), residues: 244
  sheet: -1.48 (1.76), residues: 10
  loop : -1.93 (0.53), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  49 
 HIS   0.004   0.002   HIS A  87 
 PHE   0.009   0.002   PHE A 114 
 TYR   0.016   0.002   TYR A 258 
 ARG   0.005   0.001   ARG A 214 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9363 (m-30) cc_final: 0.9100 (m-30)
REVERT: A    7 GLU cc_start: 0.8334 (pt0) cc_final: 0.8107 (pp20)
REVERT: A   70 GLN cc_start: 0.9466 (mt0) cc_final: 0.8927 (mp10)
REVERT: A   79 SER cc_start: 0.9032 (m) cc_final: 0.8503 (m)
REVERT: A  103 GLU cc_start: 0.8937 (tt0) cc_final: 0.8471 (pm20)
REVERT: A  180 MET cc_start: 0.6351 (mpp) cc_final: 0.5766 (mpp)
REVERT: A  256 ASP cc_start: 0.9255 (t70) cc_final: 0.8304 (t70)
REVERT: A  294 MET cc_start: 0.8454 (mmm) cc_final: 0.8149 (mmt)
REVERT: A  300 LEU cc_start: 0.9432 (mt) cc_final: 0.9141 (tt)
REVERT: A  321 SER cc_start: 0.9462 (m) cc_final: 0.9224 (p)
REVERT: A  362 LEU cc_start: 0.9392 (tt) cc_final: 0.8816 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1715
  time to fit residues: 14.4018
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0570
   chunk 19 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6702

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.071518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.060902 restraints weight = 14835.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.062641 restraints weight = 8981.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.063998 restraints weight = 6220.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.6091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3214  Z= 0.142
  Angle     :  0.572   6.828   4364  Z= 0.289
  Chirality :  0.038   0.148    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.138  59.107    523
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.43), residues: 387
  helix:  1.11 (0.34), residues: 236
  sheet:  None (None), residues: 0
  loop : -1.58 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 360 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.019   0.001   PHE A 267 
 TYR   0.019   0.001   TYR A 331 
 ARG   0.003   0.000   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9475 (m-30) cc_final: 0.9176 (m-30)
REVERT: A   76 LEU cc_start: 0.9447 (mt) cc_final: 0.9189 (mt)
REVERT: A  103 GLU cc_start: 0.8972 (tt0) cc_final: 0.8475 (pm20)
REVERT: A  130 MET cc_start: 0.9538 (mmp) cc_final: 0.9325 (mmm)
REVERT: A  271 LEU cc_start: 0.8845 (mm) cc_final: 0.8258 (mm)
REVERT: A  294 MET cc_start: 0.8421 (mmm) cc_final: 0.7971 (mmt)
REVERT: A  311 MET cc_start: 0.9163 (tpt) cc_final: 0.8867 (tpt)
REVERT: A  337 MET cc_start: 0.8294 (ppp) cc_final: 0.8036 (ppp)
REVERT: A  362 LEU cc_start: 0.9367 (tt) cc_final: 0.8856 (mm)
REVERT: A  381 GLU cc_start: 0.6160 (tt0) cc_final: 0.5858 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1442
  time to fit residues: 12.1279
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.072689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.061905 restraints weight = 14644.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.063674 restraints weight = 8982.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.064975 restraints weight = 6181.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.6396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3214  Z= 0.140
  Angle     :  0.569   6.356   4364  Z= 0.282
  Chirality :  0.039   0.193    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.982  58.984    523
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.43), residues: 387
  helix:  1.13 (0.34), residues: 246
  sheet:  None (None), residues: 0
  loop : -1.83 (0.48), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.013   0.001   PHE A 267 
 TYR   0.008   0.001   TYR A 331 
 ARG   0.003   0.000   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9508 (m-30) cc_final: 0.9112 (m-30)
REVERT: A   70 GLN cc_start: 0.9498 (mt0) cc_final: 0.8858 (mt0)
REVERT: A   76 LEU cc_start: 0.9393 (mt) cc_final: 0.9099 (mt)
REVERT: A  103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8465 (pm20)
REVERT: A  271 LEU cc_start: 0.8803 (mm) cc_final: 0.8206 (mm)
REVERT: A  294 MET cc_start: 0.8454 (mmm) cc_final: 0.7467 (mmm)
REVERT: A  311 MET cc_start: 0.9194 (tpt) cc_final: 0.8918 (tpt)
REVERT: A  333 PHE cc_start: 0.9080 (t80) cc_final: 0.8748 (t80)
REVERT: A  335 MET cc_start: 0.8852 (mmm) cc_final: 0.8642 (mmm)
REVERT: A  337 MET cc_start: 0.8186 (ppp) cc_final: 0.7974 (ppp)
REVERT: A  365 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8307 (mt-10)
REVERT: A  381 GLU cc_start: 0.6090 (tt0) cc_final: 0.5788 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1390
  time to fit residues: 10.5165
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.067533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.057300 restraints weight = 15483.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.059038 restraints weight = 9264.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.060232 restraints weight = 6288.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.6777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3214  Z= 0.241
  Angle     :  0.638   9.322   4364  Z= 0.327
  Chirality :  0.041   0.161    499
  Planarity :  0.004   0.026    549
  Dihedral  : 10.467  63.123    523
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.43), residues: 387
  helix:  1.41 (0.34), residues: 245
  sheet: -0.85 (1.96), residues: 10
  loop : -1.75 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  49 
 HIS   0.004   0.001   HIS A  80 
 PHE   0.014   0.002   PHE A 359 
 TYR   0.019   0.002   TYR A 258 
 ARG   0.006   0.001   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9507 (m-30) cc_final: 0.9162 (m-30)
REVERT: A   70 GLN cc_start: 0.9500 (mt0) cc_final: 0.8868 (mt0)
REVERT: A   76 LEU cc_start: 0.9439 (mt) cc_final: 0.9180 (mt)
REVERT: A  103 GLU cc_start: 0.8871 (tt0) cc_final: 0.8324 (pm20)
REVERT: A  294 MET cc_start: 0.8452 (mmm) cc_final: 0.7665 (mmm)
REVERT: A  300 LEU cc_start: 0.9593 (tt) cc_final: 0.9228 (tt)
REVERT: A  333 PHE cc_start: 0.9174 (t80) cc_final: 0.8921 (t80)
REVERT: A  335 MET cc_start: 0.8913 (mmm) cc_final: 0.8610 (mmm)
REVERT: A  365 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8285 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1354
  time to fit residues: 10.1342
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0770
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1944

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.070038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.059575 restraints weight = 14369.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.061406 restraints weight = 8500.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.062663 restraints weight = 5722.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.6942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3214  Z= 0.142
  Angle     :  0.574   7.339   4364  Z= 0.281
  Chirality :  0.040   0.182    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.061  59.134    523
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.43), residues: 387
  helix:  1.53 (0.33), residues: 247
  sheet: -0.70 (1.96), residues: 10
  loop : -1.68 (0.50), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 173 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.013   0.001   PHE A 267 
 TYR   0.011   0.001   TYR A 331 
 ARG   0.002   0.000   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9522 (m-30) cc_final: 0.9101 (m-30)
REVERT: A   56 LEU cc_start: 0.9719 (tp) cc_final: 0.9152 (pp)
REVERT: A   70 GLN cc_start: 0.9471 (mt0) cc_final: 0.8780 (mt0)
REVERT: A   76 LEU cc_start: 0.9411 (mt) cc_final: 0.9135 (mt)
REVERT: A  103 GLU cc_start: 0.8879 (tt0) cc_final: 0.8401 (pm20)
REVERT: A  129 MET cc_start: 0.8405 (mmp) cc_final: 0.8167 (ptt)
REVERT: A  294 MET cc_start: 0.8437 (mmm) cc_final: 0.7512 (mmm)
REVERT: A  300 LEU cc_start: 0.9570 (tt) cc_final: 0.9236 (tt)
REVERT: A  335 MET cc_start: 0.8864 (mmm) cc_final: 0.8633 (mmm)
REVERT: A  337 MET cc_start: 0.8271 (ppp) cc_final: 0.8070 (ppp)
REVERT: A  365 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8222 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1366
  time to fit residues: 10.5935
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.070156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.059808 restraints weight = 14492.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.061659 restraints weight = 8629.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.062902 restraints weight = 5806.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.7099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3214  Z= 0.143
  Angle     :  0.591  10.594   4364  Z= 0.284
  Chirality :  0.039   0.168    499
  Planarity :  0.003   0.023    549
  Dihedral  :  9.977  59.019    523
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.43), residues: 387
  helix:  1.67 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.60 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 173 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.011   0.001   PHE A 267 
 TYR   0.009   0.001   TYR A   8 
 ARG   0.002   0.000   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9395 (m-30) cc_final: 0.9157 (m-30)
REVERT: A   70 GLN cc_start: 0.9463 (mt0) cc_final: 0.8924 (mt0)
REVERT: A   76 LEU cc_start: 0.9402 (mt) cc_final: 0.9158 (mt)
REVERT: A  103 GLU cc_start: 0.8893 (tt0) cc_final: 0.8405 (pm20)
REVERT: A  129 MET cc_start: 0.8353 (mmp) cc_final: 0.8117 (ptt)
REVERT: A  294 MET cc_start: 0.8491 (mmm) cc_final: 0.7771 (mmm)
REVERT: A  306 ASP cc_start: 0.8569 (t0) cc_final: 0.8134 (t70)
REVERT: A  335 MET cc_start: 0.9414 (mmm) cc_final: 0.8766 (mtp)
REVERT: A  365 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8223 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1335
  time to fit residues: 9.8346
Evaluate side-chains
  48 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 34 optimal weight:    0.0000
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.071926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.061694 restraints weight = 14533.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063498 restraints weight = 8773.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.064761 restraints weight = 5936.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.7212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3214  Z= 0.134
  Angle     :  0.579   8.252   4364  Z= 0.278
  Chirality :  0.038   0.176    499
  Planarity :  0.003   0.023    549
  Dihedral  :  9.845  58.986    523
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.43), residues: 387
  helix:  1.66 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.53 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 360 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.019   0.001   PHE A  54 
 TYR   0.006   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A 127 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9480 (m-30) cc_final: 0.9236 (m-30)
REVERT: A    9 GLU cc_start: 0.8767 (pp20) cc_final: 0.8511 (pp20)
REVERT: A   26 GLU cc_start: 0.3926 (tp30) cc_final: 0.3198 (pp20)
REVERT: A   70 GLN cc_start: 0.9438 (mt0) cc_final: 0.8871 (mt0)
REVERT: A   76 LEU cc_start: 0.9425 (mt) cc_final: 0.9210 (mt)
REVERT: A  103 GLU cc_start: 0.8914 (tt0) cc_final: 0.8358 (pm20)
REVERT: A  294 MET cc_start: 0.8381 (mmm) cc_final: 0.7482 (mmm)
REVERT: A  303 MET cc_start: 0.9194 (ppp) cc_final: 0.8950 (ppp)
REVERT: A  306 ASP cc_start: 0.8482 (t0) cc_final: 0.8109 (t70)
REVERT: A  311 MET cc_start: 0.8833 (tpt) cc_final: 0.8458 (tpt)
REVERT: A  335 MET cc_start: 0.9346 (mmm) cc_final: 0.9007 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1293
  time to fit residues: 9.8803
Evaluate side-chains
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0370
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:   20.0000
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.072277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.061648 restraints weight = 14432.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063548 restraints weight = 8783.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.064897 restraints weight = 5922.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.7337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3214  Z= 0.135
  Angle     :  0.606  12.506   4364  Z= 0.286
  Chirality :  0.039   0.167    499
  Planarity :  0.003   0.023    549
  Dihedral  :  9.838  58.915    523
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.43), residues: 387
  helix:  1.60 (0.33), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.47 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 360 
 HIS   0.010   0.002   HIS A  87 
 PHE   0.012   0.001   PHE A 268 
 TYR   0.007   0.001   TYR A 258 
 ARG   0.003   0.000   ARG A 228 

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

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

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  774 Ramachandran restraints generated.
    387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9497 (m-30) cc_final: 0.9144 (m-30)
REVERT: A   26 GLU cc_start: 0.3841 (tp30) cc_final: 0.3187 (pp20)
REVERT: A   70 GLN cc_start: 0.9466 (mt0) cc_final: 0.9057 (mp10)
REVERT: A  103 GLU cc_start: 0.8873 (tt0) cc_final: 0.8302 (pm20)
REVERT: A  294 MET cc_start: 0.8413 (mmm) cc_final: 0.7924 (tpt)
REVERT: A  303 MET cc_start: 0.9210 (ppp) cc_final: 0.8964 (ppp)
REVERT: A  306 ASP cc_start: 0.8488 (t0) cc_final: 0.8119 (t70)
REVERT: A  311 MET cc_start: 0.8814 (tpt) cc_final: 0.8482 (tpt)
REVERT: A  335 MET cc_start: 0.9364 (mmm) cc_final: 0.9060 (mtp)
REVERT: A  355 MET cc_start: 0.7158 (tpt) cc_final: 0.6899 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1564
  time to fit residues: 12.2494
Evaluate side-chains
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.070856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.060610 restraints weight = 14541.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.062463 restraints weight = 8740.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.063754 restraints weight = 5895.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.7416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3214  Z= 0.142
  Angle     :  0.581   6.319   4364  Z= 0.285
  Chirality :  0.039   0.168    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.875  58.865    523
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.43), residues: 387
  helix:  1.59 (0.33), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.44 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 360 
 HIS   0.008   0.002   HIS A  87 
 PHE   0.011   0.001   PHE A 268 
 TYR   0.008   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1284.89 seconds
wall clock time: 23 minutes 50.14 seconds (1430.14 seconds total)