Starting phenix.real_space_refine
on Fri Sep 11 00:09:40 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2026/6jc3_9793.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 6}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
  Time building chain proxies: 0.90, per 1000 atoms: 0.29
  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: 0.24
  Conformation dependent library (CDL) restraints added in 86.6 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: 0.39
  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: 0.47

  Time building geometry restraints manager: 0.31 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: 4197
        2.95 -     5.91: 134
        5.91 -     8.86: 21
        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: 1648
       15.35 -    30.71: 220
       30.71 -    46.06: 55
       46.06 -    61.41: 21
       61.41 -    76.77: 4
  Dihedral angle restraints: 1948
    sinusoidal: 813
      harmonic: 1135
  Sorted by residual:
  dihedral pdb=" C4'   U N  36 "
           pdb=" C3'   U N  36 "
           pdb=" C2'   U N  36 "
           pdb=" C1'   U N  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.43   72.78     1      3.10e+00 1.04e-01 7.03e+02
  dihedral pdb=" O4'   U N  36 "
           pdb=" C4'   U N  36 "
           pdb=" C3'   U N  36 "
           pdb=" C2'   U N  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   25.29  -60.44     1      4.00e+00 6.25e-02 3.04e+02
  dihedral pdb=" O4'   U N  36 "
           pdb=" C2'   U N  36 "
           pdb=" C1'   U N  36 "
           pdb=" C3'   U N  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -94.41  -35.92  -58.48     3      3.80e+00 6.93e-02 1.48e+02
  ... (remaining 1945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 434
       0.100 -    0.200: 51
       0.200 -    0.300: 9
       0.300 -    0.400: 3
       0.400 -    0.500: 2
  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=" P     U N  37 "
            pdb=" OP1   U N  37 "
            pdb=" OP2   U N  37 "
            pdb=" O5'   U N  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.61   -0.43 2.00e-01 2.50e+01 4.67e+00
  chirality pdb=" P     U N  35 "
            pdb=" OP1   U N  35 "
            pdb=" OP2   U N  35 "
            pdb=" O5'   U N  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.51   -0.34 2.00e-01 2.50e+01 2.92e+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:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.820
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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= 0.520
  Angle     :  1.367  14.766   4364  Z= 0.817
  Chirality :  0.078   0.500    499
  Planarity :  0.008   0.064    549
  Dihedral  : 16.164  76.766   1216
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.009   0.002   ARG A  69 
 TYR   0.020   0.004   TYR A 249 
 PHE   0.023   0.003   PHE A 145 
 TRP   0.012   0.004   TRP A 173 
 HIS   0.003   0.002   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01023 /  0.52 ( 3214)
  covalent geometry    : angle       1.36674 /  0.82 ( 4364)
  hydrogen bonds       : bond        0.19060 / 11.92 (  159)
  hydrogen bonds       : angle       7.86710 /  5.34 (  459)

*********************** 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  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ARG cc_start: 0.8912 (ttp-110) cc_final: 0.8487 (tpt170)
REVERT: A  103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8565 (pm20)
REVERT: A  135 LEU cc_start: 0.8057 (mt) cc_final: 0.7492 (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: 0.9567 (t70) cc_final: 0.9322 (t0)
REVERT: A  258 TYR cc_start: 0.8391 (m-80) cc_final: 0.8163 (m-80)
REVERT: A  278 LYS cc_start: 0.7222 (mttt) cc_final: 0.6323 (tppt)
REVERT: A  282 LEU cc_start: 0.9302 (tt) cc_final: 0.8882 (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: 0.8909 (tpp)
REVERT: A  365 GLU cc_start: 0.8539 (tp30) cc_final: 0.8274 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 138
  average time/residue: 0.0783
  time to fit residues: 12.4899
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  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3236 r_free = 0.3236 target = 0.072597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.061351 restraints weight = 14774.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.063344 restraints weight = 8970.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.064749 restraints weight = 6122.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.065792 restraints weight = 4498.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.066517 restraints weight = 3493.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.4407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3214  Z= 0.162
  Angle     :  0.743   7.823   4364  Z= 0.361
  Chirality :  0.051   0.335    499
  Planarity :  0.005   0.041    549
  Dihedral  : 10.336 123.315    499
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.40), residues: 387
  helix: -0.50 (0.30), residues: 235
  sheet: -1.99 (1.44), residues: 10
  loop : -1.87 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 124 
 TYR   0.006   0.001   TYR A 327 
 PHE   0.014   0.002   PHE A  54 
 TRP   0.013   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 3214)
  covalent geometry    : angle       0.74278 /  0.36 ( 4364)
  hydrogen bonds       : bond        0.04511 /  2.85 (  159)
  hydrogen bonds       : angle       4.72619 /  3.21 (  459)

*********************** 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  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9481 (m-30) cc_final: 0.9100 (m-30)
REVERT: A  103 GLU cc_start: 0.8945 (tt0) cc_final: 0.8280 (pm20)
REVERT: A  173 TRP cc_start: 0.9492 (m100) cc_final: 0.9033 (m100)
REVERT: A  178 LYS cc_start: 0.9496 (mmtm) cc_final: 0.9287 (mppt)
REVERT: A  231 LEU cc_start: 0.9574 (mt) cc_final: 0.9330 (mt)
REVERT: A  256 ASP cc_start: 0.9157 (t70) cc_final: 0.8056 (t70)
REVERT: A  261 ASN cc_start: 0.8020 (m-40) cc_final: 0.7213 (m-40)
REVERT: A  271 LEU cc_start: 0.8956 (mm) cc_final: 0.8225 (mm)
REVERT: A  300 LEU cc_start: 0.9483 (mt) cc_final: 0.9268 (mt)
REVERT: A  326 GLU cc_start: 0.8696 (pm20) cc_final: 0.8428 (pm20)
REVERT: A  337 MET cc_start: 0.8421 (ppp) cc_final: 0.8208 (ppp)
REVERT: A  365 GLU cc_start: 0.8335 (tp30) cc_final: 0.8012 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0719
  time to fit residues: 7.3272
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.0010
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0040
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  87 HIS
A 292 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.061981 restraints weight = 14717.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.063835 restraints weight = 8760.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.065006 restraints weight = 5938.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.066058 restraints weight = 4454.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.066730 restraints weight = 3454.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.5460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3214  Z= 0.120
  Angle     :  0.664   7.855   4364  Z= 0.318
  Chirality :  0.048   0.334    499
  Planarity :  0.004   0.030    549
  Dihedral  :  9.964 127.047    499
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.30
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.43), residues: 387
  helix:  0.79 (0.34), residues: 238
  sheet: -1.29 (1.89), residues: 10
  loop : -1.66 (0.52), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 214 
 TYR   0.020   0.001   TYR A 331 
 PHE   0.016   0.001   PHE A  54 
 TRP   0.012   0.002   TRP A  49 
 HIS   0.003   0.001   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 3214)
  covalent geometry    : angle       0.66437 /  0.32 ( 4364)
  hydrogen bonds       : bond        0.03599 /  2.24 (  159)
  hydrogen bonds       : angle       3.94999 /  2.68 (  459)

*********************** 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
  75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9448 (m-30) cc_final: 0.9033 (m-30)
REVERT: A   56 LEU cc_start: 0.9690 (tp) cc_final: 0.9173 (pp)
REVERT: A   76 LEU cc_start: 0.9354 (mt) cc_final: 0.9042 (mt)
REVERT: A   84 MET cc_start: 0.8552 (mtm) cc_final: 0.8324 (mtt)
REVERT: A  103 GLU cc_start: 0.8968 (tt0) cc_final: 0.8428 (pm20)
REVERT: A  231 LEU cc_start: 0.9635 (mt) cc_final: 0.9279 (tt)
REVERT: A  237 ARG cc_start: 0.8806 (mtp-110) cc_final: 0.8069 (ttm110)
REVERT: A  271 LEU cc_start: 0.8897 (mm) cc_final: 0.8193 (mm)
REVERT: A  294 MET cc_start: 0.8405 (mmm) cc_final: 0.8108 (mmt)
REVERT: A  300 LEU cc_start: 0.9399 (mt) cc_final: 0.9161 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0537
  time to fit residues: 4.9948
Evaluate side-chains
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    0.3980
   chunk 13 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.0788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.070404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.059939 restraints weight = 14530.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.061712 restraints weight = 8876.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.063021 restraints weight = 6036.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063921 restraints weight = 4442.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.064558 restraints weight = 3476.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.5973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3214  Z= 0.124
  Angle     :  0.642   8.584   4364  Z= 0.300
  Chirality :  0.049   0.370    499
  Planarity :  0.003   0.020    549
  Dihedral  :  9.761 126.934    499
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.44), residues: 387
  helix:  1.30 (0.34), residues: 238
  sheet: -1.17 (1.99), residues: 10
  loop : -1.57 (0.51), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 127 
 TYR   0.010   0.001   TYR A 331 
 PHE   0.007   0.001   PHE A 114 
 TRP   0.012   0.003   TRP A  49 
 HIS   0.003   0.001   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 3214)
  covalent geometry    : angle       0.64240 /  0.30 ( 4364)
  hydrogen bonds       : bond        0.03354 /  2.13 (  159)
  hydrogen bonds       : angle       3.87036 /  2.64 (  459)

*********************** 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
  70 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.120 
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: 0.9505 (m-30) cc_final: 0.9116 (m-30)
REVERT: A  103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8409 (pm20)
REVERT: A  271 LEU cc_start: 0.8871 (mm) cc_final: 0.8180 (mm)
REVERT: A  294 MET cc_start: 0.8440 (mmm) cc_final: 0.8114 (mmt)
REVERT: A  300 LEU cc_start: 0.9443 (mt) cc_final: 0.9226 (tt)
REVERT: A  311 MET cc_start: 0.9283 (ttm) cc_final: 0.9068 (tpp)
REVERT: A  326 GLU cc_start: 0.8695 (pm20) cc_final: 0.8425 (pm20)
REVERT: A  333 PHE cc_start: 0.9156 (t80) cc_final: 0.8901 (t80)
REVERT: A  365 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8269 (mt-10)
REVERT: A  381 GLU cc_start: 0.6507 (tt0) cc_final: 0.6204 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0552
  time to fit residues: 4.9034
Evaluate side-chains
  51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 210 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.067440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.057668 restraints weight = 15568.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.059371 restraints weight = 9501.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.060518 restraints weight = 6481.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.061340 restraints weight = 4804.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.061868 restraints weight = 3773.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.6571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3214  Z= 0.171
  Angle     :  0.730  10.119   4364  Z= 0.345
  Chirality :  0.054   0.461    499
  Planarity :  0.004   0.031    549
  Dihedral  :  9.925 128.617    499
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.45), residues: 387
  helix:  1.43 (0.34), residues: 239
  sheet: -0.98 (1.99), residues: 10
  loop : -1.46 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 127 
 TYR   0.015   0.001   TYR A 258 
 PHE   0.015   0.002   PHE A 267 
 TRP   0.019   0.003   TRP A 173 
 HIS   0.003   0.001   HIS A  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.17 ( 3214)
  covalent geometry    : angle       0.73036 /  0.34 ( 4364)
  hydrogen bonds       : bond        0.03676 /  2.39 (  159)
  hydrogen bonds       : angle       4.07779 /  2.80 (  459)

*********************** 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
  63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9487 (m-30) cc_final: 0.9155 (m-30)
REVERT: A   70 GLN cc_start: 0.9457 (mt0) cc_final: 0.8986 (mp10)
REVERT: A   76 LEU cc_start: 0.9313 (mt) cc_final: 0.9043 (mt)
REVERT: A  103 GLU cc_start: 0.8885 (tt0) cc_final: 0.8396 (pm20)
REVERT: A  311 MET cc_start: 0.9316 (ttm) cc_final: 0.9097 (tpp)
REVERT: A  326 GLU cc_start: 0.8741 (pm20) cc_final: 0.8428 (pm20)
REVERT: A  333 PHE cc_start: 0.9121 (t80) cc_final: 0.8863 (t80)
REVERT: A  365 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8232 (mt-10)
REVERT: A  375 ASN cc_start: 0.9100 (t0) cc_final: 0.8831 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0557
  time to fit residues: 4.3252
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  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.5586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.069205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.059037 restraints weight = 14877.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.060740 restraints weight = 9053.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.061998 restraints weight = 6205.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062857 restraints weight = 4562.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.063377 restraints weight = 3571.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.6781

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= 0.112
  Angle     :  0.674  10.229   4364  Z= 0.304
  Chirality :  0.052   0.445    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.711 126.659    499
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.44), residues: 387
  helix:  1.68 (0.34), residues: 239
  sheet: -0.82 (1.93), residues: 10
  loop : -1.38 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.019   0.001   PHE A  54 
 TRP   0.014   0.002   TRP A 173 
 HIS   0.002   0.001   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 3214)
  covalent geometry    : angle       0.67447 /  0.30 ( 4364)
  hydrogen bonds       : bond        0.03082 /  1.97 (  159)
  hydrogen bonds       : angle       3.67996 /  2.54 (  459)

*********************** 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  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9477 (m-30) cc_final: 0.9212 (m-30)
REVERT: A    9 GLU cc_start: 0.8856 (pp20) cc_final: 0.8395 (pp20)
REVERT: A   76 LEU cc_start: 0.9289 (mt) cc_final: 0.9049 (mt)
REVERT: A  103 GLU cc_start: 0.8875 (tt0) cc_final: 0.8386 (pm20)
REVERT: A  294 MET cc_start: 0.8286 (mmm) cc_final: 0.7973 (mmt)
REVERT: A  300 LEU cc_start: 0.9489 (tt) cc_final: 0.9140 (tt)
REVERT: A  311 MET cc_start: 0.9255 (ttm) cc_final: 0.9016 (tpp)
REVERT: A  326 GLU cc_start: 0.8737 (pm20) cc_final: 0.8415 (pm20)
REVERT: A  337 MET cc_start: 0.8250 (ppp) cc_final: 0.8014 (ppp)
REVERT: A  365 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8222 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0650
  time to fit residues: 5.0586
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  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    1.8584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.069236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.059212 restraints weight = 15159.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.060855 restraints weight = 9178.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.062135 restraints weight = 6316.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.063033 restraints weight = 4608.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.063683 restraints weight = 3561.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.7024

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= 0.114
  Angle     :  0.690  10.390   4364  Z= 0.308
  Chirality :  0.053   0.485    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.587 126.675    499
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.45), residues: 387
  helix:  1.84 (0.34), residues: 239
  sheet: -0.75 (1.96), residues: 10
  loop : -1.24 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.012   0.001   PHE A 267 
 TRP   0.014   0.002   TRP A 173 
 HIS   0.002   0.001   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 3214)
  covalent geometry    : angle       0.68974 /  0.31 ( 4364)
  hydrogen bonds       : bond        0.03032 /  1.92 (  159)
  hydrogen bonds       : angle       3.57713 /  2.48 (  459)

*********************** 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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9466 (m-30) cc_final: 0.9198 (m-30)
REVERT: A    9 GLU cc_start: 0.8896 (pp20) cc_final: 0.8464 (pp20)
REVERT: A   26 GLU cc_start: 0.3920 (tp30) cc_final: 0.3172 (pp20)
REVERT: A   56 LEU cc_start: 0.9717 (tp) cc_final: 0.9290 (pp)
REVERT: A   76 LEU cc_start: 0.9296 (mt) cc_final: 0.9016 (mt)
REVERT: A  103 GLU cc_start: 0.8903 (tt0) cc_final: 0.8269 (pm20)
REVERT: A  129 MET cc_start: 0.8844 (ptp) cc_final: 0.8494 (ptt)
REVERT: A  237 ARG cc_start: 0.8953 (mtp-110) cc_final: 0.8138 (ttm110)
REVERT: A  294 MET cc_start: 0.8314 (mmm) cc_final: 0.8003 (mmt)
REVERT: A  300 LEU cc_start: 0.9558 (tt) cc_final: 0.9175 (tt)
REVERT: A  311 MET cc_start: 0.9293 (ttm) cc_final: 0.8986 (tpp)
REVERT: A  326 GLU cc_start: 0.8772 (pm20) cc_final: 0.8512 (pm20)
REVERT: A  333 PHE cc_start: 0.8993 (t80) cc_final: 0.8724 (t80)
REVERT: A  365 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8278 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0522
  time to fit residues: 4.0115
Evaluate side-chains
  51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.067834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.058006 restraints weight = 15294.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.059838 restraints weight = 9222.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.061135 restraints weight = 6178.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.062061 restraints weight = 4450.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062574 restraints weight = 3400.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.7309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3214  Z= 0.113
  Angle     :  0.683  10.652   4364  Z= 0.304
  Chirality :  0.053   0.509    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.556 126.864    499
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.45), residues: 387
  helix:  1.97 (0.34), residues: 239
  sheet: -0.52 (1.97), residues: 10
  loop : -1.14 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A 267 
 TRP   0.012   0.002   TRP A 173 
 HIS   0.003   0.001   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 3214)
  covalent geometry    : angle       0.68318 /  0.30 ( 4364)
  hydrogen bonds       : bond        0.02913 /  1.85 (  159)
  hydrogen bonds       : angle       3.53544 /  2.46 (  459)

*********************** 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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9467 (m-30) cc_final: 0.9188 (m-30)
REVERT: A    9 GLU cc_start: 0.8853 (pp20) cc_final: 0.8453 (pp20)
REVERT: A   26 GLU cc_start: 0.4051 (tp30) cc_final: 0.3271 (pp20)
REVERT: A   56 LEU cc_start: 0.9717 (tp) cc_final: 0.9288 (pp)
REVERT: A   76 LEU cc_start: 0.9353 (mt) cc_final: 0.9079 (mt)
REVERT: A  103 GLU cc_start: 0.8915 (tt0) cc_final: 0.8288 (pm20)
REVERT: A  129 MET cc_start: 0.8797 (ptp) cc_final: 0.8310 (ptt)
REVERT: A  237 ARG cc_start: 0.8934 (mtp-110) cc_final: 0.8106 (ttm110)
REVERT: A  294 MET cc_start: 0.8369 (mmm) cc_final: 0.8046 (mmt)
REVERT: A  300 LEU cc_start: 0.9523 (tt) cc_final: 0.9086 (tt)
REVERT: A  311 MET cc_start: 0.9221 (ttm) cc_final: 0.8923 (tpp)
REVERT: A  326 GLU cc_start: 0.8879 (pm20) cc_final: 0.8580 (pm20)
REVERT: A  333 PHE cc_start: 0.9024 (t80) cc_final: 0.8754 (t80)
REVERT: A  365 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8269 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0567
  time to fit residues: 4.3739
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  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0870
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0970
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.4360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  87 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.067705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.058102 restraints weight = 15071.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059872 restraints weight = 9059.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.061105 restraints weight = 6085.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.061999 restraints weight = 4436.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.062667 restraints weight = 3419.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.7464

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= 0.125
  Angle     :  0.709  10.589   4364  Z= 0.315
  Chirality :  0.054   0.513    499
  Planarity :  0.003   0.022    549
  Dihedral  :  9.579 127.382    499
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.45), residues: 387
  helix:  1.99 (0.34), residues: 239
  sheet: -0.49 (1.96), residues: 10
  loop : -1.22 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.012   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A 267 
 TRP   0.011   0.002   TRP A 173 
 HIS   0.002   0.001   HIS A  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 ( 3214)
  covalent geometry    : angle       0.70892 /  0.32 ( 4364)
  hydrogen bonds       : bond        0.03011 /  1.93 (  159)
  hydrogen bonds       : angle       3.64510 /  2.53 (  459)

*********************** 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
  59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9474 (m-30) cc_final: 0.9213 (m-30)
REVERT: A    9 GLU cc_start: 0.8833 (pp20) cc_final: 0.8411 (pp20)
REVERT: A   26 GLU cc_start: 0.4103 (tp30) cc_final: 0.3439 (pp20)
REVERT: A   56 LEU cc_start: 0.9729 (tp) cc_final: 0.9295 (pp)
REVERT: A   76 LEU cc_start: 0.9337 (mt) cc_final: 0.9067 (mt)
REVERT: A  103 GLU cc_start: 0.8825 (tt0) cc_final: 0.8270 (pm20)
REVERT: A  129 MET cc_start: 0.8815 (ptp) cc_final: 0.8341 (ptt)
REVERT: A  180 MET cc_start: 0.6838 (mpp) cc_final: 0.6086 (mtm)
REVERT: A  237 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8081 (ttm110)
REVERT: A  294 MET cc_start: 0.8456 (mmm) cc_final: 0.8091 (mmt)
REVERT: A  311 MET cc_start: 0.9294 (ttm) cc_final: 0.8934 (tpp)
REVERT: A  326 GLU cc_start: 0.8752 (pm20) cc_final: 0.8488 (pm20)
REVERT: A  329 GLN cc_start: 0.9289 (mp10) cc_final: 0.9064 (mp10)
REVERT: A  333 PHE cc_start: 0.8974 (t80) cc_final: 0.8724 (t80)
REVERT: A  337 MET cc_start: 0.7985 (ppp) cc_final: 0.7773 (ppp)
REVERT: A  365 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8321 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0524
  time to fit residues: 3.8825
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  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0050
   overall best weight:    0.8596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 210 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.069502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.059878 restraints weight = 14194.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.061732 restraints weight = 8430.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.063040 restraints weight = 5611.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.063992 restraints weight = 4028.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.064638 restraints weight = 3068.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.7562

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= 0.102
  Angle     :  0.676  10.599   4364  Z= 0.296
  Chirality :  0.052   0.515    499
  Planarity :  0.003   0.023    549
  Dihedral  :  9.521 125.940    499
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.44), residues: 387
  helix:  1.95 (0.34), residues: 239
  sheet:  None (None), residues: 0
  loop : -1.26 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 127 
 TYR   0.007   0.001   TYR A 327 
 PHE   0.012   0.001   PHE A 267 
 TRP   0.013   0.003   TRP A 360 
 HIS   0.001   0.000   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 ( 3214)
  covalent geometry    : angle       0.67592 /  0.30 ( 4364)
  hydrogen bonds       : bond        0.02732 /  1.70 (  159)
  hydrogen bonds       : angle       3.51696 /  2.45 (  459)

********************** 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
  63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9463 (m-30) cc_final: 0.9179 (m-30)
REVERT: A    9 GLU cc_start: 0.8847 (pp20) cc_final: 0.8473 (pp20)
REVERT: A   26 GLU cc_start: 0.4131 (tp30) cc_final: 0.3360 (pp20)
REVERT: A   56 LEU cc_start: 0.9714 (tp) cc_final: 0.9284 (pp)
REVERT: A   76 LEU cc_start: 0.9328 (mt) cc_final: 0.9090 (mt)
REVERT: A  103 GLU cc_start: 0.8833 (tt0) cc_final: 0.8355 (pm20)
REVERT: A  129 MET cc_start: 0.8681 (ptp) cc_final: 0.8199 (ptt)
REVERT: A  180 MET cc_start: 0.6392 (mpp) cc_final: 0.5678 (mtm)
REVERT: A  237 ARG cc_start: 0.8948 (mtp-110) cc_final: 0.8100 (ttm110)
REVERT: A  294 MET cc_start: 0.8352 (mmm) cc_final: 0.8058 (mmt)
REVERT: A  306 ASP cc_start: 0.8607 (t0) cc_final: 0.8248 (t0)
REVERT: A  311 MET cc_start: 0.9245 (ttm) cc_final: 0.8849 (tpp)
REVERT: A  326 GLU cc_start: 0.8886 (pm20) cc_final: 0.8563 (pm20)
REVERT: A  329 GLN cc_start: 0.9357 (mp10) cc_final: 0.9030 (mp10)
REVERT: A  333 PHE cc_start: 0.8803 (t80) cc_final: 0.8569 (t80)
REVERT: A  337 MET cc_start: 0.8011 (ppp) cc_final: 0.7730 (ppp)
REVERT: A  355 MET cc_start: 0.7242 (tpt) cc_final: 0.6883 (tpp)
REVERT: A  362 LEU cc_start: 0.9107 (tt) cc_final: 0.8626 (mm)
REVERT: A  365 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8259 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0516
  time to fit residues: 4.0948
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  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3164 r_free = 0.3164 target = 0.069002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.059371 restraints weight = 14663.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.061257 restraints weight = 8698.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.062590 restraints weight = 5763.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.063540 restraints weight = 4130.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.064235 restraints weight = 3150.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.7643

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= 0.108
  Angle     :  0.673  10.361   4364  Z= 0.298
  Chirality :  0.052   0.502    499
  Planarity :  0.003   0.023    549
  Dihedral  :  9.497 126.274    499
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.33
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.44), residues: 387
  helix:  2.00 (0.34), residues: 239
  sheet:  None (None), residues: 0
  loop : -1.26 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 127 
 TYR   0.009   0.001   TYR A 258 
 PHE   0.010   0.001   PHE A 267 
 TRP   0.010   0.002   TRP A  49 
 HIS   0.006   0.002   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.11 ( 3214)
  covalent geometry    : angle       0.67296 /  0.30 ( 4364)
  hydrogen bonds       : bond        0.02818 /  1.80 (  159)
  hydrogen bonds       : angle       3.58176 /  2.51 (  459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 635.12 seconds
wall clock time: 11 minutes 34.35 seconds (694.35 seconds total)