Starting phenix.real_space_refine
on Thu Mar  6 10:38:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jc3_9793/03_2025/6jc3_9793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jc3_9793/03_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_9793/03_2025/6jc3_9793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jc3_9793/03_2025/6jc3_9793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jc3_9793/03_2025/6jc3_9793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jc3_9793/03_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-5624/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: 2.98, per 1000 atoms: 0.94
  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: 0.69
  Conformation dependent library (CDL) restraints added in 322.1 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: 1.15
  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: 0.79

  Time building geometry restraints manager: 0.84 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:             163.100
  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:                     14.200
  Find NCS groups from input model:        0.040
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  180.360
-------------------------------------------------------------------------------
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  : 0.321 
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: 0.2086
  time to fit residues: 32.8124
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  : 0.328 
-------------------------------------------------------------------------------
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 = 8719.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.067776 restraints weight = 5993.993|
|-----------------------------------------------------------------------------|
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  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9498 (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: 0.7462 (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: 0.6848 (t)
REVERT: A  256 ASP cc_start: 0.9204 (t70) cc_final: 0.8372 (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: 0.8511 (mmm) cc_final: 0.8121 (mmt)
REVERT: A  302 ARG cc_start: 0.3145 (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: 0.8337 (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: 0.1713
  time to fit residues: 17.4494
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  : 0.322 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3114 r_free = 0.3114 target = 0.066954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.056811 restraints weight = 15386.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.058525 restraints weight = 9215.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.059709 restraints weight = 6220.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.5803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3214  Z= 0.327
  Angle     :  0.739  11.768   4364  Z= 0.387
  Chirality :  0.042   0.178    499
  Planarity :  0.005   0.052    549
  Dihedral  : 10.808  63.894    523
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  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: -0.65 (0.42), residues: 387
  helix:  0.44 (0.32), residues: 244
  sheet: -1.57 (1.75), residues: 10
  loop : -1.93 (0.54), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  49 
 HIS   0.006   0.002   HIS A  87 
 PHE   0.011   0.002   PHE A 359 
 TYR   0.020   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
  64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9369 (m-30) cc_final: 0.9131 (m-30)
REVERT: A    7 GLU cc_start: 0.8365 (pt0) cc_final: 0.8145 (pp20)
REVERT: A   55 CYS cc_start: 0.9562 (m) cc_final: 0.9361 (m)
REVERT: A   70 GLN cc_start: 0.9481 (mt0) cc_final: 0.8953 (mp10)
REVERT: A   76 LEU cc_start: 0.9463 (mt) cc_final: 0.9232 (mt)
REVERT: A  103 GLU cc_start: 0.8942 (tt0) cc_final: 0.8455 (pm20)
REVERT: A  129 MET cc_start: 0.8889 (ptt) cc_final: 0.8561 (mmp)
REVERT: A  130 MET cc_start: 0.9579 (mmp) cc_final: 0.9374 (mmp)
REVERT: A  256 ASP cc_start: 0.9267 (t70) cc_final: 0.8561 (t0)
REVERT: A  300 LEU cc_start: 0.9436 (mt) cc_final: 0.9144 (tt)
REVERT: A  321 SER cc_start: 0.9507 (m) cc_final: 0.9281 (p)
REVERT: A  362 LEU cc_start: 0.9431 (tt) cc_final: 0.8832 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1557
  time to fit residues: 12.1947
Evaluate side-chains
  45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0370
   chunk 23 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.8066

-------------------------------------------------------------------------------
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 = 0.3138 r_free = 0.3138 target = 0.067928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.057540 restraints weight = 15245.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.059321 restraints weight = 9120.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.060562 restraints weight = 6169.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.6239

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= 0.189
  Angle     :  0.606   8.797   4364  Z= 0.311
  Chirality :  0.039   0.153    499
  Planarity :  0.003   0.023    549
  Dihedral  : 10.540  59.306    523
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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:  0.05 (0.44), residues: 387
  helix:  1.05 (0.34), residues: 245
  sheet: -1.07 (1.96), residues: 10
  loop : -1.85 (0.53), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.007   0.001   PHE A 359 
 TYR   0.016   0.001   TYR A 331 
 ARG   0.005   0.001   ARG A 239 

*********************** 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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9413 (m-30) cc_final: 0.9109 (m-30)
REVERT: A   70 GLN cc_start: 0.9486 (mt0) cc_final: 0.9008 (mp10)
REVERT: A  103 GLU cc_start: 0.8885 (tt0) cc_final: 0.8398 (pm20)
REVERT: A  129 MET cc_start: 0.8906 (ptt) cc_final: 0.8664 (mmp)
REVERT: A  130 MET cc_start: 0.9620 (mmp) cc_final: 0.9400 (mmp)
REVERT: A  271 LEU cc_start: 0.8858 (mm) cc_final: 0.8261 (mm)
REVERT: A  300 LEU cc_start: 0.9478 (mt) cc_final: 0.9245 (tt)
REVERT: A  311 MET cc_start: 0.9338 (tpt) cc_final: 0.9076 (tpt)
REVERT: A  321 SER cc_start: 0.9538 (m) cc_final: 0.9216 (p)
REVERT: A  326 GLU cc_start: 0.9136 (pm20) cc_final: 0.8805 (pm20)
REVERT: A  337 MET cc_start: 0.8502 (ppp) cc_final: 0.8255 (ppp)
REVERT: A  362 LEU cc_start: 0.9371 (tt) cc_final: 0.8835 (mm)
REVERT: A  365 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8262 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1590
  time to fit residues: 11.8275
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  : 0.355 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 5 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0000
   chunk 2 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8186

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.070681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.060655 restraints weight = 14757.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.062401 restraints weight = 8687.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.063648 restraints weight = 5834.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.6507

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= 0.138
  Angle     :  0.545   6.621   4364  Z= 0.276
  Chirality :  0.039   0.191    499
  Planarity :  0.003   0.023    549
  Dihedral  : 10.084  59.181    523
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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:  0.51 (0.43), residues: 387
  helix:  1.46 (0.34), residues: 237
  sheet:  None (None), residues: 0
  loop : -1.55 (0.49), residues: 150

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   0.008   0.001   PHE A 114 
 TYR   0.012   0.001   TYR A 207 
 ARG   0.004   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  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9382 (m-30) cc_final: 0.9098 (m-30)
REVERT: A    7 GLU cc_start: 0.8255 (pt0) cc_final: 0.7977 (pp20)
REVERT: A   56 LEU cc_start: 0.9707 (tp) cc_final: 0.9200 (pp)
REVERT: A   70 GLN cc_start: 0.9504 (mt0) cc_final: 0.9074 (mp10)
REVERT: A   76 LEU cc_start: 0.9428 (mt) cc_final: 0.9137 (mt)
REVERT: A  103 GLU cc_start: 0.8927 (tt0) cc_final: 0.8402 (pm20)
REVERT: A  271 LEU cc_start: 0.8841 (mm) cc_final: 0.8278 (mm)
REVERT: A  294 MET cc_start: 0.8573 (mmm) cc_final: 0.7668 (mmm)
REVERT: A  333 PHE cc_start: 0.9137 (t80) cc_final: 0.8861 (t80)
REVERT: A  335 MET cc_start: 0.8872 (mmm) cc_final: 0.8638 (mmm)
REVERT: A  365 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8185 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1393
  time to fit residues: 10.5786
Evaluate side-chains
  50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.1700

-------------------------------------------------------------------------------
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 = 0.3186 r_free = 0.3186 target = 0.070653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.060212 restraints weight = 15064.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.061934 restraints weight = 9015.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.063204 restraints weight = 6128.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.6708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3214  Z= 0.139
  Angle     :  0.566  10.302   4364  Z= 0.278
  Chirality :  0.038   0.174    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.016  59.073    523
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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:  0.35 (0.43), residues: 387
  helix:  1.41 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -2.01 (0.47), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 173 
 HIS   0.002   0.001   HIS A  87 
 PHE   0.008   0.001   PHE A 268 
 TYR   0.008   0.001   TYR A 207 
 ARG   0.003   0.000   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
  64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9512 (m-30) cc_final: 0.9176 (m-30)
REVERT: A   70 GLN cc_start: 0.9487 (mt0) cc_final: 0.9094 (mp10)
REVERT: A   76 LEU cc_start: 0.9389 (mt) cc_final: 0.9131 (mt)
REVERT: A  103 GLU cc_start: 0.8943 (tt0) cc_final: 0.8403 (pm20)
REVERT: A  129 MET cc_start: 0.8788 (ptt) cc_final: 0.8317 (ptt)
REVERT: A  130 MET cc_start: 0.9512 (mmp) cc_final: 0.9310 (mmm)
REVERT: A  294 MET cc_start: 0.8510 (mmm) cc_final: 0.7615 (mmm)
REVERT: A  300 LEU cc_start: 0.9560 (tt) cc_final: 0.9233 (tt)
REVERT: A  326 GLU cc_start: 0.9274 (pm20) cc_final: 0.9012 (pm20)
REVERT: A  333 PHE cc_start: 0.9124 (t80) cc_final: 0.8832 (t80)
REVERT: A  335 MET cc_start: 0.8835 (mmm) cc_final: 0.8575 (mmm)
REVERT: A  365 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8156 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1541
  time to fit residues: 12.0597
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  : 0.361 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0970
   chunk 30 optimal weight:    8.9990
   overall best weight:    2.7584

-------------------------------------------------------------------------------
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 = 0.3140 r_free = 0.3140 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.057842 restraints weight = 14907.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.059605 restraints weight = 8705.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.060829 restraints weight = 5809.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.6993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3214  Z= 0.183
  Angle     :  0.602   8.087   4364  Z= 0.302
  Chirality :  0.040   0.177    499
  Planarity :  0.003   0.023    549
  Dihedral  : 10.235  59.875    523
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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:  0.66 (0.43), residues: 387
  helix:  1.62 (0.34), residues: 245
  sheet: -0.59 (1.90), residues: 10
  loop : -1.82 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  49 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.021   0.001   PHE A  54 
 TYR   0.014   0.001   TYR A 258 
 ARG   0.002   0.000   ARG A 222 

*********************** 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
  66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9535 (m-30) cc_final: 0.9169 (m-30)
REVERT: A    7 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8518 (pt0)
REVERT: A   26 GLU cc_start: 0.4066 (tp30) cc_final: 0.3241 (pp20)
REVERT: A   70 GLN cc_start: 0.9468 (mt0) cc_final: 0.9065 (mp10)
REVERT: A   76 LEU cc_start: 0.9421 (mt) cc_final: 0.9161 (mt)
REVERT: A  103 GLU cc_start: 0.8807 (tt0) cc_final: 0.8279 (pm20)
REVERT: A  129 MET cc_start: 0.8859 (ptt) cc_final: 0.8345 (ptt)
REVERT: A  130 MET cc_start: 0.9563 (mmp) cc_final: 0.9334 (mmm)
REVERT: A  294 MET cc_start: 0.8448 (mmm) cc_final: 0.7604 (mmm)
REVERT: A  300 LEU cc_start: 0.9524 (tt) cc_final: 0.9149 (tt)
REVERT: A  306 ASP cc_start: 0.8583 (t0) cc_final: 0.8144 (t70)
REVERT: A  333 PHE cc_start: 0.9184 (t80) cc_final: 0.8980 (t80)
REVERT: A  335 MET cc_start: 0.8853 (mmm) cc_final: 0.8596 (mmm)
REVERT: A  365 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8244 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1370
  time to fit residues: 11.2108
Evaluate side-chains
  50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 8 optimal weight:    0.0370
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0670
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7998

-------------------------------------------------------------------------------
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 = 0.3180 r_free = 0.3180 target = 0.069939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.059916 restraints weight = 14466.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.061725 restraints weight = 8529.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.063002 restraints weight = 5682.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.7166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3214  Z= 0.134
  Angle     :  0.583   6.561   4364  Z= 0.283
  Chirality :  0.039   0.172    499
  Planarity :  0.003   0.024    549
  Dihedral  :  9.983  59.123    523
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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:  0.71 (0.43), residues: 387
  helix:  1.69 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.86 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 360 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.009   0.001   PHE A 268 
 TYR   0.008   0.001   TYR A 258 
 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
  68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9562 (m-30) cc_final: 0.9131 (m-30)
REVERT: A   15 GLN cc_start: 0.8964 (tt0) cc_final: 0.8368 (tm-30)
REVERT: A   56 LEU cc_start: 0.9712 (tp) cc_final: 0.9148 (pp)
REVERT: A   76 LEU cc_start: 0.9377 (mt) cc_final: 0.9115 (mt)
REVERT: A  103 GLU cc_start: 0.8910 (tt0) cc_final: 0.8291 (pm20)
REVERT: A  130 MET cc_start: 0.9564 (mmp) cc_final: 0.9319 (mmm)
REVERT: A  294 MET cc_start: 0.8530 (mmm) cc_final: 0.7681 (mmm)
REVERT: A  303 MET cc_start: 0.9120 (ppp) cc_final: 0.8908 (ppp)
REVERT: A  306 ASP cc_start: 0.8588 (t0) cc_final: 0.8151 (t70)
REVERT: A  326 GLU cc_start: 0.9171 (pm20) cc_final: 0.8937 (pm20)
REVERT: A  333 PHE cc_start: 0.9096 (t80) cc_final: 0.8871 (t80)
REVERT: A  337 MET cc_start: 0.8091 (ppp) cc_final: 0.7857 (ppp)
REVERT: A  365 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8206 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1417
  time to fit residues: 11.9278
Evaluate side-chains
  52 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0970
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6376

-------------------------------------------------------------------------------
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 = 0.3202 r_free = 0.3202 target = 0.070925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.060776 restraints weight = 14562.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.062603 restraints weight = 8576.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.063869 restraints weight = 5720.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.7313

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= 0.134
  Angle     :  0.591   8.312   4364  Z= 0.287
  Chirality :  0.039   0.171    499
  Planarity :  0.003   0.024    549
  Dihedral  :  9.890  59.038    523
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  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:  0.75 (0.44), residues: 387
  helix:  1.72 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.84 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 360 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.012   0.001   PHE A 268 
 TYR   0.007   0.001   TYR A 258 
 ARG   0.008   0.000   ARG A 222 

*********************** 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
  63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9690 (tp) cc_final: 0.9143 (pp)
REVERT: A   70 GLN cc_start: 0.9475 (mt0) cc_final: 0.8887 (mt0)
REVERT: A   76 LEU cc_start: 0.9378 (mt) cc_final: 0.9124 (mt)
REVERT: A  103 GLU cc_start: 0.8884 (tt0) cc_final: 0.8274 (pm20)
REVERT: A  130 MET cc_start: 0.9567 (mmp) cc_final: 0.9351 (mmm)
REVERT: A  294 MET cc_start: 0.8495 (mmm) cc_final: 0.7683 (mmm)
REVERT: A  303 MET cc_start: 0.9119 (ppp) cc_final: 0.8892 (ppp)
REVERT: A  306 ASP cc_start: 0.8518 (t0) cc_final: 0.8126 (t70)
REVERT: A  326 GLU cc_start: 0.9221 (pm20) cc_final: 0.8944 (pm20)
REVERT: A  335 MET cc_start: 0.9317 (mmm) cc_final: 0.9055 (mtp)
REVERT: A  337 MET cc_start: 0.8183 (ppp) cc_final: 0.7952 (ppp)
REVERT: A  365 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8222 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1303
  time to fit residues: 10.2964
Evaluate side-chains
  45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.7186

-------------------------------------------------------------------------------
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 = 0.3153 r_free = 0.3153 target = 0.068644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.058490 restraints weight = 14890.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.060299 restraints weight = 8839.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.061518 restraints weight = 5933.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.7504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3214  Z= 0.224
  Angle     :  0.647   8.406   4364  Z= 0.324
  Chirality :  0.041   0.172    499
  Planarity :  0.003   0.021    549
  Dihedral  : 10.322  61.140    523
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  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:  0.66 (0.44), residues: 387
  helix:  1.60 (0.34), residues: 247
  sheet: -0.45 (1.94), residues: 10
  loop : -1.83 (0.53), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A  80 
 PHE   0.010   0.001   PHE A 268 
 TYR   0.018   0.002   TYR A 258 
 ARG   0.008   0.001   ARG A 222 

********************** 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
  57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9547 (m-30) cc_final: 0.9207 (m-30)
REVERT: A   70 GLN cc_start: 0.9482 (mt0) cc_final: 0.8906 (mt0)
REVERT: A   76 LEU cc_start: 0.9389 (mt) cc_final: 0.9135 (mt)
REVERT: A  103 GLU cc_start: 0.8838 (tt0) cc_final: 0.8259 (pm20)
REVERT: A  129 MET cc_start: 0.8818 (ptt) cc_final: 0.8221 (ptt)
REVERT: A  294 MET cc_start: 0.8488 (mmm) cc_final: 0.7655 (mmm)
REVERT: A  300 LEU cc_start: 0.9459 (tt) cc_final: 0.9054 (tt)
REVERT: A  311 MET cc_start: 0.8830 (tpt) cc_final: 0.8624 (tpt)
REVERT: A  335 MET cc_start: 0.9398 (mmm) cc_final: 0.9009 (mtp)
REVERT: A  365 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8228 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1257
  time to fit residues: 9.1444
Evaluate side-chains
  44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0040
   chunk 38 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.9796

-------------------------------------------------------------------------------
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 = 0.3205 r_free = 0.3205 target = 0.071005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.060951 restraints weight = 14454.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.062749 restraints weight = 8651.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.064009 restraints weight = 5824.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.7603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3214  Z= 0.139
  Angle     :  0.597   7.078   4364  Z= 0.292
  Chirality :  0.040   0.175    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.001  59.125    523
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  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:  0.61 (0.43), residues: 387
  helix:  1.57 (0.33), residues: 247
  sheet:  None (None), residues: 0
  loop : -1.79 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 360 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.019   0.001   PHE A  54 
 TYR   0.009   0.001   TYR A 258 
 ARG   0.006   0.000   ARG A 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1742.81 seconds
wall clock time: 31 minutes 26.04 seconds (1886.04 seconds total)