Starting phenix.real_space_refine
on Wed Sep 17 06:08:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jc3_9793/09_2025/6jc3_9793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jc3_9793/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2025/6jc3_9793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2025/6jc3_9793.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2025/6jc3_9793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jc3_9793/09_2025/6jc3_9793.map"
  }
  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-2.0-5805/lib/python3.9/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: {'RNA': 6}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
  Time building chain proxies: 1.09, per 1000 atoms: 0.35
  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: 0.29
  Conformation dependent library (CDL) restraints added in 119.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.41
  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: 0.34

  Time building geometry restraints manager: 0.37 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:             2.630
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.390
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.340
-------------------------------------------------------------------------------
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= 0.522
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
  covalent geometry    : bond        0.01022 ( 3214)
  covalent geometry    : angle       1.35023 ( 4364)
  hydrogen bonds       : bond        0.19060 (  159)
  hydrogen bonds       : angle       7.86710 (  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  : 0.132 
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: 0.9568 (t70) cc_final: 0.9323 (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: 0.9301 (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: 0.0940
  time to fit residues: 14.8759
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  : 0.120 
-------------------------------------------------------------------------------
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...

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 = 0.3238 r_free = 0.3238 target = 0.072733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.061498 restraints weight = 14892.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.063480 restraints weight = 8991.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.064872 restraints weight = 6113.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.065886 restraints weight = 4501.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.066629 restraints weight = 3502.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3214  Z= 0.159
  Angle     :  0.661   6.794   4364  Z= 0.348
  Chirality :  0.041   0.156    499
  Planarity :  0.004   0.041    549
  Dihedral  : 10.847  60.859    523
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  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 aren not related in a simple way.
  whole: -1.63 (0.40), residues: 387
  helix: -0.49 (0.30), residues: 235
  sheet: -1.99 (1.43), residues: 10
  loop : -1.89 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 124 
 TYR   0.006   0.001   TYR A 327 
 PHE   0.015   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
  covalent geometry    : bond        0.00345 ( 3214)
  covalent geometry    : angle       0.66072 ( 4364)
  hydrogen bonds       : bond        0.04502 (  159)
  hydrogen bonds       : angle       4.74363 (  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
  88 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9476 (m-30) cc_final: 0.9112 (m-30)
REVERT: A  103 GLU cc_start: 0.8944 (tt0) cc_final: 0.8258 (pm20)
REVERT: A  173 TRP cc_start: 0.9496 (m100) cc_final: 0.9155 (m100)
REVERT: A  231 LEU cc_start: 0.9577 (mt) cc_final: 0.9305 (tt)
REVERT: A  256 ASP cc_start: 0.9155 (t70) cc_final: 0.8089 (t70)
REVERT: A  261 ASN cc_start: 0.7935 (m-40) cc_final: 0.7202 (m-40)
REVERT: A  271 LEU cc_start: 0.8969 (mm) cc_final: 0.8250 (mm)
REVERT: A  300 LEU cc_start: 0.9475 (mt) cc_final: 0.9263 (mt)
REVERT: A  302 ARG cc_start: 0.3265 (mtt-85) cc_final: 0.3059 (ttm170)
REVERT: A  326 GLU cc_start: 0.8723 (pm20) cc_final: 0.8419 (pm20)
REVERT: A  337 MET cc_start: 0.8431 (ppp) cc_final: 0.8216 (ppp)
REVERT: A  365 GLU cc_start: 0.8323 (tp30) cc_final: 0.8016 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0791
  time to fit residues: 8.0910
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  : 0.132 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.066579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.055949 restraints weight = 15438.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.057744 restraints weight = 9113.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.058992 restraints weight = 6123.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.059899 restraints weight = 4495.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.060412 restraints weight = 3525.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.5754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3214  Z= 0.221
  Angle     :  0.709  10.529   4364  Z= 0.369
  Chirality :  0.042   0.204    499
  Planarity :  0.005   0.055    549
  Dihedral  : 10.754  61.666    523
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  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 aren not related in a simple way.
  whole: -0.18 (0.43), residues: 387
  helix:  0.77 (0.33), residues: 236
  sheet: -1.51 (1.84), residues: 10
  loop : -1.49 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 214 
 TYR   0.014   0.002   TYR A 258 
 PHE   0.010   0.002   PHE A 114 
 TRP   0.015   0.002   TRP A  49 
 HIS   0.003   0.001   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 3214)
  covalent geometry    : angle       0.70899 ( 4364)
  hydrogen bonds       : bond        0.04416 (  159)
  hydrogen bonds       : angle       4.49578 (  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
  66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9375 (m-30) cc_final: 0.9099 (m-30)
REVERT: A   76 LEU cc_start: 0.9382 (mt) cc_final: 0.9133 (mt)
REVERT: A  103 GLU cc_start: 0.8928 (tt0) cc_final: 0.8452 (pm20)
REVERT: A  256 ASP cc_start: 0.9110 (t70) cc_final: 0.8334 (t70)
REVERT: A  294 MET cc_start: 0.8403 (mmm) cc_final: 0.8122 (mmt)
REVERT: A  300 LEU cc_start: 0.9425 (mt) cc_final: 0.9102 (tt)
REVERT: A  326 GLU cc_start: 0.9128 (pm20) cc_final: 0.8813 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0622
  time to fit residues: 5.0597
Evaluate side-chains
  47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.3148 r_free = 0.3148 target = 0.068709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.058071 restraints weight = 15091.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.059849 restraints weight = 8988.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.061126 restraints weight = 6092.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.062054 restraints weight = 4491.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.062641 restraints weight = 3510.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3214  Z= 0.125
  Angle     :  0.597   8.571   4364  Z= 0.302
  Chirality :  0.040   0.186    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.431  59.287    523
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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 aren not related in a simple way.
  whole:  0.22 (0.44), residues: 387
  helix:  1.14 (0.34), residues: 237
  sheet: -1.20 (1.98), residues: 10
  loop : -1.50 (0.53), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.007   0.001   PHE A 114 
 TRP   0.009   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3214)
  covalent geometry    : angle       0.59657 ( 4364)
  hydrogen bonds       : bond        0.03526 (  159)
  hydrogen bonds       : angle       4.12876 (  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
  62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9517 (m-30) cc_final: 0.9127 (m-30)
REVERT: A  103 GLU cc_start: 0.8995 (tt0) cc_final: 0.8396 (pm20)
REVERT: A  129 MET cc_start: 0.8440 (mmp) cc_final: 0.8170 (ptt)
REVERT: A  271 LEU cc_start: 0.8841 (mm) cc_final: 0.8260 (mm)
REVERT: A  300 LEU cc_start: 0.9454 (mt) cc_final: 0.9169 (tt)
REVERT: A  311 MET cc_start: 0.9385 (ttt) cc_final: 0.9021 (ppp)
REVERT: A  321 SER cc_start: 0.9525 (m) cc_final: 0.9223 (p)
REVERT: A  333 PHE cc_start: 0.9186 (t80) cc_final: 0.8852 (t80)
REVERT: A  337 MET cc_start: 0.8350 (ppp) cc_final: 0.8130 (ppp)
REVERT: A  365 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8292 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0508
  time to fit residues: 4.0197
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  : 0.122 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 37 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0470
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:   20.0000
   overall best weight:    1.3682

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN

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 = 0.070067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.059700 restraints weight = 15015.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.061532 restraints weight = 9065.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.062802 restraints weight = 6124.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.063683 restraints weight = 4498.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.064349 restraints weight = 3519.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.6495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3214  Z= 0.107
  Angle     :  0.559   7.718   4364  Z= 0.279
  Chirality :  0.039   0.169    499
  Planarity :  0.003   0.022    549
  Dihedral  : 10.145  59.196    523
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.44), residues: 387
  helix:  1.41 (0.34), residues: 239
  sheet: -1.09 (1.99), residues: 10
  loop : -1.63 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.007   0.001   TYR A 207 
 PHE   0.007   0.001   PHE A 114 
 TRP   0.011   0.002   TRP A  49 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3214)
  covalent geometry    : angle       0.55910 ( 4364)
  hydrogen bonds       : bond        0.03175 (  159)
  hydrogen bonds       : angle       3.82023 (  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  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9486 (m-30) cc_final: 0.9093 (m-30)
REVERT: A   76 LEU cc_start: 0.9406 (mt) cc_final: 0.9153 (mt)
REVERT: A  103 GLU cc_start: 0.8931 (tt0) cc_final: 0.8310 (pm20)
REVERT: A  129 MET cc_start: 0.8321 (mmp) cc_final: 0.7973 (ptt)
REVERT: A  237 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8539 (ttp-110)
REVERT: A  271 LEU cc_start: 0.8858 (mm) cc_final: 0.8335 (mm)
REVERT: A  294 MET cc_start: 0.8305 (mmm) cc_final: 0.7467 (mmm)
REVERT: A  311 MET cc_start: 0.9392 (ttt) cc_final: 0.9062 (ppp)
REVERT: A  326 GLU cc_start: 0.8814 (pm20) cc_final: 0.8525 (pm20)
REVERT: A  333 PHE cc_start: 0.9152 (t80) cc_final: 0.8851 (t80)
REVERT: A  335 MET cc_start: 0.9451 (mmm) cc_final: 0.8728 (mtp)
REVERT: A  365 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8237 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0760
  time to fit residues: 5.7933
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  : 0.119 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 2 optimal weight:   30.0000
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 12 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.065063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.055262 restraints weight = 15193.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.056992 restraints weight = 8913.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.058181 restraints weight = 6000.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.058969 restraints weight = 4421.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.059642 restraints weight = 3523.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.7041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3214  Z= 0.244
  Angle     :  0.700  11.856   4364  Z= 0.363
  Chirality :  0.043   0.166    499
  Planarity :  0.004   0.026    549
  Dihedral  : 10.846  64.536    523
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.44), residues: 387
  helix:  1.37 (0.34), residues: 237
  sheet: -0.85 (1.92), residues: 10
  loop : -1.62 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 222 
 TYR   0.023   0.002   TYR A 258 
 PHE   0.013   0.002   PHE A 359 
 TRP   0.011   0.002   TRP A  49 
 HIS   0.005   0.002   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 3214)
  covalent geometry    : angle       0.70005 ( 4364)
  hydrogen bonds       : bond        0.04196 (  159)
  hydrogen bonds       : angle       4.52091 (  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
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9516 (m-30) cc_final: 0.9213 (m-30)
REVERT: A   26 GLU cc_start: 0.4103 (tp30) cc_final: 0.3281 (pp20)
REVERT: A   76 LEU cc_start: 0.9387 (mt) cc_final: 0.9130 (mt)
REVERT: A  103 GLU cc_start: 0.8803 (tt0) cc_final: 0.8200 (pm20)
REVERT: A  129 MET cc_start: 0.8441 (mmp) cc_final: 0.8219 (ptt)
REVERT: A  300 LEU cc_start: 0.9532 (tt) cc_final: 0.9110 (tt)
REVERT: A  326 GLU cc_start: 0.8873 (pm20) cc_final: 0.8589 (pm20)
REVERT: A  333 PHE cc_start: 0.9173 (t80) cc_final: 0.8868 (t80)
REVERT: A  335 MET cc_start: 0.9468 (mmm) cc_final: 0.8737 (mtp)
REVERT: A  365 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8218 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0571
  time to fit residues: 3.8767
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  : 0.102 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0670
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    1.6724

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 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 = 0.3119 r_free = 0.3119 target = 0.067133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.057472 restraints weight = 15274.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.059110 restraints weight = 9081.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.060329 restraints weight = 6192.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.061204 restraints weight = 4512.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.061851 restraints weight = 3510.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.7157

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= 0.113
  Angle     :  0.588   9.040   4364  Z= 0.293
  Chirality :  0.041   0.176    499
  Planarity :  0.003   0.025    549
  Dihedral  : 10.460  59.283    523
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.45), residues: 387
  helix:  1.60 (0.35), residues: 239
  sheet: -0.74 (1.94), residues: 10
  loop : -1.59 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 127 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.009   0.001   PHE A 268 
 TRP   0.010   0.002   TRP A  49 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3214)
  covalent geometry    : angle       0.58798 ( 4364)
  hydrogen bonds       : bond        0.03431 (  159)
  hydrogen bonds       : angle       3.97648 (  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
  62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9509 (m-30) cc_final: 0.9268 (m-30)
REVERT: A    9 GLU cc_start: 0.8974 (pp20) cc_final: 0.8486 (pp20)
REVERT: A   76 LEU cc_start: 0.9342 (mt) cc_final: 0.9107 (mt)
REVERT: A  103 GLU cc_start: 0.8795 (tt0) cc_final: 0.8234 (pm20)
REVERT: A  129 MET cc_start: 0.8390 (mmp) cc_final: 0.8140 (ptt)
REVERT: A  173 TRP cc_start: 0.9481 (m100) cc_final: 0.9157 (m100)
REVERT: A  231 LEU cc_start: 0.9656 (mt) cc_final: 0.9320 (tt)
REVERT: A  237 ARG cc_start: 0.8988 (mtp-110) cc_final: 0.8557 (ttp-110)
REVERT: A  294 MET cc_start: 0.8488 (mmm) cc_final: 0.7680 (mmm)
REVERT: A  326 GLU cc_start: 0.8837 (pm20) cc_final: 0.8499 (pm20)
REVERT: A  329 GLN cc_start: 0.9270 (mp10) cc_final: 0.9046 (mp10)
REVERT: A  333 PHE cc_start: 0.9165 (t80) cc_final: 0.8919 (t80)
REVERT: A  335 MET cc_start: 0.9479 (mmm) cc_final: 0.8725 (mtp)
REVERT: A  365 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8240 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0668
  time to fit residues: 5.1034
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  : 0.116 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 33 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.068288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.058420 restraints weight = 15425.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.060250 restraints weight = 9089.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.061460 restraints weight = 6057.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.062344 restraints weight = 4397.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.063034 restraints weight = 3402.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.7336

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= 0.105
  Angle     :  0.571   8.204   4364  Z= 0.283
  Chirality :  0.040   0.167    499
  Planarity :  0.003   0.025    549
  Dihedral  : 10.148  59.183    523
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.45), residues: 387
  helix:  1.75 (0.35), residues: 239
  sheet:  None (None), residues: 0
  loop : -1.57 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.009   0.001   TYR A 258 
 PHE   0.021   0.001   PHE A  54 
 TRP   0.010   0.002   TRP A  49 
 HIS   0.004   0.002   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 3214)
  covalent geometry    : angle       0.57089 ( 4364)
  hydrogen bonds       : bond        0.03185 (  159)
  hydrogen bonds       : angle       3.77826 (  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  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9459 (m-30) cc_final: 0.9230 (m-30)
REVERT: A    9 GLU cc_start: 0.8857 (pp20) cc_final: 0.8422 (pp20)
REVERT: A   76 LEU cc_start: 0.9370 (mt) cc_final: 0.9159 (mt)
REVERT: A  103 GLU cc_start: 0.8806 (tt0) cc_final: 0.8239 (pm20)
REVERT: A  173 TRP cc_start: 0.9414 (m100) cc_final: 0.9029 (m100)
REVERT: A  237 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8349 (ttp-110)
REVERT: A  294 MET cc_start: 0.8241 (mmm) cc_final: 0.7935 (tpt)
REVERT: A  326 GLU cc_start: 0.8975 (pm20) cc_final: 0.8598 (pm20)
REVERT: A  335 MET cc_start: 0.9403 (mmm) cc_final: 0.8593 (mtp)
REVERT: A  365 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8216 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0687
  time to fit residues: 5.1233
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  : 0.125 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0470
   chunk 12 optimal weight:    0.2980
   chunk 1 optimal weight:    0.0870
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.2658

-------------------------------------------------------------------------------
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 = 0.3158 r_free = 0.3158 target = 0.069159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.059533 restraints weight = 14951.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.061318 restraints weight = 8921.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.062553 restraints weight = 5944.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.063452 restraints weight = 4315.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.064104 restraints weight = 3324.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.7506

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= 0.103
  Angle     :  0.582   7.806   4364  Z= 0.287
  Chirality :  0.039   0.164    499
  Planarity :  0.003   0.025    549
  Dihedral  : 10.041  59.151    523
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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 aren not related in a simple way.
  whole:  0.81 (0.45), residues: 387
  helix:  1.69 (0.35), residues: 239
  sheet:  None (None), residues: 0
  loop : -1.47 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 127 
 TYR   0.008   0.001   TYR A 258 
 PHE   0.008   0.001   PHE A 114 
 TRP   0.013   0.002   TRP A 360 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3214)
  covalent geometry    : angle       0.58179 ( 4364)
  hydrogen bonds       : bond        0.03107 (  159)
  hydrogen bonds       : angle       3.72417 (  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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9473 (m-30) cc_final: 0.9220 (m-30)
REVERT: A    9 GLU cc_start: 0.8844 (pp20) cc_final: 0.8422 (pp20)
REVERT: A   76 LEU cc_start: 0.9378 (mt) cc_final: 0.9172 (mt)
REVERT: A  103 GLU cc_start: 0.8848 (tt0) cc_final: 0.8298 (pm20)
REVERT: A  173 TRP cc_start: 0.9440 (m100) cc_final: 0.9075 (m100)
REVERT: A  237 ARG cc_start: 0.8967 (mtp-110) cc_final: 0.8339 (ttp-110)
REVERT: A  294 MET cc_start: 0.8355 (mmm) cc_final: 0.7992 (tpt)
REVERT: A  306 ASP cc_start: 0.8696 (t0) cc_final: 0.8328 (t70)
REVERT: A  326 GLU cc_start: 0.8979 (pm20) cc_final: 0.8560 (pm20)
REVERT: A  335 MET cc_start: 0.9298 (mmm) cc_final: 0.8904 (mtp)
REVERT: A  365 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8255 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0691
  time to fit residues: 5.0770
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  : 0.110 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0370
   chunk 28 optimal weight:    0.4980
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.8462

-------------------------------------------------------------------------------
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 = 0.3160 r_free = 0.3160 target = 0.069242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.059306 restraints weight = 14906.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.061158 restraints weight = 8886.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.062397 restraints weight = 5919.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.063221 restraints weight = 4283.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.063909 restraints weight = 3359.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.7588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3214  Z= 0.111
  Angle     :  0.574   8.148   4364  Z= 0.284
  Chirality :  0.040   0.162    499
  Planarity :  0.003   0.024    549
  Dihedral  : 10.061  59.105    523
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.30
  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 aren not related in a simple way.
  whole:  0.91 (0.45), residues: 387
  helix:  1.75 (0.35), residues: 239
  sheet: -0.53 (1.94), residues: 10
  loop : -1.40 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.007   0.001   PHE A 114 
 TRP   0.013   0.002   TRP A 360 
 HIS   0.002   0.001   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 3214)
  covalent geometry    : angle       0.57427 ( 4364)
  hydrogen bonds       : bond        0.03110 (  159)
  hydrogen bonds       : angle       3.77737 (  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
  59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9473 (m-30) cc_final: 0.9233 (m-30)
REVERT: A    9 GLU cc_start: 0.8820 (pp20) cc_final: 0.8376 (pp20)
REVERT: A   76 LEU cc_start: 0.9404 (mt) cc_final: 0.9164 (mt)
REVERT: A  103 GLU cc_start: 0.8911 (tt0) cc_final: 0.8323 (pm20)
REVERT: A  173 TRP cc_start: 0.9447 (m100) cc_final: 0.9129 (m100)
REVERT: A  237 ARG cc_start: 0.8983 (mtp-110) cc_final: 0.8374 (ttp-110)
REVERT: A  294 MET cc_start: 0.8312 (mmm) cc_final: 0.6976 (mmm)
REVERT: A  327 TYR cc_start: 0.6408 (m-10) cc_final: 0.5294 (m-10)
REVERT: A  329 GLN cc_start: 0.9374 (mp10) cc_final: 0.9157 (mp10)
REVERT: A  335 MET cc_start: 0.9259 (mmm) cc_final: 0.8887 (mtp)
REVERT: A  355 MET cc_start: 0.7025 (tpt) cc_final: 0.6706 (tpp)
REVERT: A  365 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8237 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0660
  time to fit residues: 4.7460
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  : 0.127 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0010
   chunk 3 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.7792

-------------------------------------------------------------------------------
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 = 0.3155 r_free = 0.3155 target = 0.069108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.059334 restraints weight = 15288.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.061139 restraints weight = 9131.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.062332 restraints weight = 6148.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.063215 restraints weight = 4499.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.063906 restraints weight = 3483.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.7631

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= 0.109
  Angle     :  0.586   8.243   4364  Z= 0.288
  Chirality :  0.040   0.163    499
  Planarity :  0.003   0.024    549
  Dihedral  : 10.041  59.106    523
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.46
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.45), residues: 387
  helix:  1.72 (0.34), residues: 239
  sheet: -0.53 (1.94), residues: 10
  loop : -1.33 (0.55), 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   0.008   0.001   PHE A 114 
 TRP   0.010   0.002   TRP A 360 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3214)
  covalent geometry    : angle       0.58585 ( 4364)
  hydrogen bonds       : bond        0.03101 (  159)
  hydrogen bonds       : angle       3.75909 (  459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 663.53 seconds
wall clock time: 12 minutes 5.60 seconds (725.60 seconds total)