Starting phenix.real_space_refine
on Sat May  2 08:42:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9okj_70566/05_2026/9okj_70566.map"
  }
  resolution = 2.68
  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=   0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     Cl      2      4.86       5
     C    2479      2.51       5
     N     626      2.21       5
     O     637      1.98       5
     F      10      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3787
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 479, 3733
          Classifications: {'peptide': 479}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 465}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'X3U': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1248  SG  CYS A 297      37.163  47.834  40.025  1.00 57.97           S

  Time building chain proxies: 1.00, per 1000 atoms: 0.26
  Number of scatterers: 3787
  At special positions: 0
  Unit cell: (76.582, 72.688, 79.178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      33     16.00
     F      10      9.00
     O     637      8.00
     N     626      7.00
     C    2479      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: 0.31
  Conformation dependent library (CDL) restraints added in 95.0 milliseconds
  

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  866

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      84.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 160
      removed outlier: 3.511A  pdb=" N   ALA A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 188
      removed outlier: 3.718A  pdb=" N   ALA A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 205 through 226
      removed outlier: 3.799A  pdb=" N   LEU A 209 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 250
      removed outlier: 3.588A  pdb=" N   SER A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 270
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.533A  pdb=" N   SER A 278 " --> pdb=" O   PRO A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 4.044A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 319
      removed outlier: 4.396A  pdb=" N   GLY A 319 " --> pdb=" O   PRO A 316 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 316 through 319'
    Processing helix  chain 'A' and resid 332 through 341
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 357 through 364
    Processing helix  chain 'A' and resid 366 through 385
    Processing helix  chain 'A' and resid 416 through 438
    Processing helix  chain 'A' and resid 443 through 481
      removed outlier: 3.837A  pdb=" N   VAL A 466 " --> pdb=" O   TYR A 462 " (cutoff:3.500A)
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 594 through 623
      Proline residue:  A 610  - end of helix
      removed outlier: 4.746A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   LYS A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 642
      removed outlier: 3.598A  pdb=" N   MET A 627 " --> pdb=" O   GLY A 623 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 642 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 645
      No H-bonds generated for 'chain 'A' and resid 643 through 645'
    Processing helix  chain 'A' and resid 647 through 677
      removed outlier: 4.350A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   TYR A 677 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 707
    Processing helix  chain 'A' and resid 712 through 731
      removed outlier: 4.433A  pdb=" N   ILE A 716 " --> pdb=" O   LYS A 712 " (cutoff:3.500A)

    294 hydrogen bonds defined for protein.
    876 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1150
        1.34 -     1.45: 639
        1.45 -     1.57: 2046
        1.57 -     1.69: 0
        1.69 -     1.81: 57
  Bond restraints: 3892
  Sorted by residual:
  bond pdb=" C22 X3U A 802 "
       pdb=" N06 X3U A 802 "
    ideal  model  delta    sigma   weight residual
    1.440  1.345  0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C04 X3U A 801 "
       pdb=" S23 X3U A 801 "
    ideal  model  delta    sigma   weight residual
    1.817  1.727  0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C22 X3U A 801 "
       pdb=" N06 X3U A 801 "
    ideal  model  delta    sigma   weight residual
    1.440  1.351  0.089 2.00e-02 2.50e+03 1.98e+01
  bond pdb=" C04 X3U A 802 "
       pdb=" S23 X3U A 802 "
    ideal  model  delta    sigma   weight residual
    1.817  1.730  0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C18 X3U A 802 "
       pdb=" N09 X3U A 802 "
    ideal  model  delta    sigma   weight residual
    1.402  1.340  0.062 2.00e-02 2.50e+03 9.55e+00
  ... (remaining 3887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 5043
        1.19 -     2.39: 176
        2.39 -     3.58: 41
        3.58 -     4.78: 15
        4.78 -     5.97: 4
  Bond angle restraints: 5279
  Sorted by residual:
  angle pdb=" N   ASN A 612 "
        pdb=" CA  ASN A 612 "
        pdb=" C   ASN A 612 "
      ideal   model   delta    sigma   weight residual
     112.23  109.66    2.57 1.26e+00 6.30e-01 4.17e+00
  angle pdb=" F14 X3U A 801 "
        pdb=" C13 X3U A 801 "
        pdb=" F15 X3U A 801 "
      ideal   model   delta    sigma   weight residual
     101.39  107.36   -5.97 3.00e+00 1.11e-01 3.96e+00
  angle pdb=" C   GLY A 709 "
        pdb=" N   ILE A 710 "
        pdb=" CA  ILE A 710 "
      ideal   model   delta    sigma   weight residual
     122.97  121.05    1.92 9.80e-01 1.04e+00 3.84e+00
  angle pdb=" N   GLY A 325 "
        pdb=" CA  GLY A 325 "
        pdb=" C   GLY A 325 "
      ideal   model   delta    sigma   weight residual
     113.30  118.97   -5.67 2.90e+00 1.19e-01 3.82e+00
  angle pdb=" F14 X3U A 802 "
        pdb=" C13 X3U A 802 "
        pdb=" F15 X3U A 802 "
      ideal   model   delta    sigma   weight residual
     101.39  107.17   -5.78 3.00e+00 1.11e-01 3.72e+00
  ... (remaining 5274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.09: 2190
       33.09 -    66.18: 34
       66.18 -    99.27: 8
       99.27 -   132.36: 1
      132.36 -   165.46: 1
  Dihedral angle restraints: 2234
    sinusoidal: 878
      harmonic: 1356
  Sorted by residual:
  dihedral pdb=" C01 X3U A 802 "
           pdb=" C03 X3U A 802 "
           pdb=" O02 X3U A 802 "
           pdb=" C04 X3U A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      71.94  -93.52  165.46     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C01 X3U A 801 "
           pdb=" C03 X3U A 801 "
           pdb=" O02 X3U A 801 "
           pdb=" C04 X3U A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      71.94 -171.94 -116.12     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" CA  PHE A 707 "
           pdb=" C   PHE A 707 "
           pdb=" N   VAL A 708 "
           pdb=" CA  VAL A 708 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.23  -16.77     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 2231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 489
       0.049 -    0.099: 74
       0.099 -    0.148: 7
       0.148 -    0.197: 0
       0.197 -    0.247: 2
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" C11 X3U A 802 "
            pdb=" C10 X3U A 802 "
            pdb=" C12 X3U A 802 "
            pdb=" C17 X3U A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.78   -2.54   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C11 X3U A 801 "
            pdb=" C10 X3U A 801 "
            pdb=" C12 X3U A 801 "
            pdb=" C17 X3U A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.78   -2.54   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  PHE A 245 "
            pdb=" N   PHE A 245 "
            pdb=" C   PHE A 245 "
            pdb=" CB  PHE A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 569 not shown)

  Planarity restraints: 645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 X3U A 802 "   -0.061 2.00e-02 2.50e+03   4.87e-02 3.56e+01
        pdb=" C10 X3U A 802 "    0.051 2.00e-02 2.50e+03
        pdb=" C17 X3U A 802 "   -0.073 2.00e-02 2.50e+03
        pdb=" C18 X3U A 802 "    0.027 2.00e-02 2.50e+03
        pdb=" N09 X3U A 802 "    0.018 2.00e-02 2.50e+03
        pdb=" O19 X3U A 802 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 X3U A 801 "    0.030 2.00e-02 2.50e+03   2.28e-02 7.77e+00
        pdb=" C10 X3U A 801 "   -0.010 2.00e-02 2.50e+03
        pdb=" C17 X3U A 801 "    0.031 2.00e-02 2.50e+03
        pdb=" C18 X3U A 801 "   -0.021 2.00e-02 2.50e+03
        pdb=" N09 X3U A 801 "   -0.025 2.00e-02 2.50e+03
        pdb=" O19 X3U A 801 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 609 "    0.022 5.00e-02 4.00e+02   3.29e-02 1.73e+00
        pdb=" N   PRO A 610 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 610 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 610 "    0.019 5.00e-02 4.00e+02
  ... (remaining 642 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1230
        2.84 -     3.35: 3879
        3.35 -     3.87: 6541
        3.87 -     4.38: 7432
        4.38 -     4.90: 12733
  Nonbonded interactions: 31815
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 462 "
            pdb=" OG1 THR A 465 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OE1 GLU A 282 "
            pdb=" OG  SER A 357 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   ILE A 703 "
            pdb=" OG  SER A 706 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" OD2 ASP A 227 "
            pdb=" OG1 THR A 684 "
     model   vdw
     2.393 3.040
  ... (remaining 31810 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             7.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.220
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:7.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
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      :  0.005   0.095   3892  Z= 0.260
  Angle     :  0.594   5.971   5279  Z= 0.316
  Chirality :  0.037   0.247    572
  Planarity :  0.004   0.049    645
  Dihedral  : 14.377 165.455   1368
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 0.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.55 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.38), residues: 471
  helix:  2.18 (0.25), residues: 378
  sheet:  None (None), residues: 0
  loop : -0.60 (0.63), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 228 
 TYR   0.015   0.001   TYR A 417 
 PHE   0.011   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 3892)
  covalent geometry    : angle       0.59422 ( 5279)
  hydrogen bonds       : bond        0.11400 (  294)
  hydrogen bonds       : angle       4.73051 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  206 MET cc_start: 0.7011 (tpp) cc_final: 0.6053 (ttt)
REVERT: A  251 PHE cc_start: 0.8752 (m-80) cc_final: 0.8537 (m-80)
REVERT: A  366 LYS cc_start: 0.8543 (mttm) cc_final: 0.8185 (mtmm)
REVERT: A  382 MET cc_start: 0.8493 (mmt) cc_final: 0.8218 (mmt)
REVERT: A  442 GLU cc_start: 0.8105 (pt0) cc_final: 0.7894 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.5920
  time to fit residues: 48.0593
Evaluate side-chains
  53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0060
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.135775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.105383 restraints weight = 3819.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.55
r_work: 0.2985 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3892  Z= 0.145
  Angle     :  0.494   4.773   5279  Z= 0.262
  Chirality :  0.038   0.136    572
  Planarity :  0.004   0.032    645
  Dihedral  : 13.682 167.119    565
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  8.27 %
    Favored  : 88.63 %
  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:  3.51 (0.38), residues: 471
  helix:  2.93 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.55 (0.64), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 682 
 TYR   0.015   0.001   TYR A 462 
 PHE   0.021   0.002   PHE A 245 
 TRP   0.009   0.001   TRP A 333 
 HIS   0.002   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3892)
  covalent geometry    : angle       0.49397 ( 5279)
  hydrogen bonds       : bond        0.05054 (  294)
  hydrogen bonds       : angle       3.65569 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  206 MET cc_start: 0.7138 (tpp) cc_final: 0.6166 (ttm)
REVERT: A  233 GLN cc_start: 0.8074 (tp40) cc_final: 0.7853 (tp40)
REVERT: A  382 MET cc_start: 0.8637 (mmt) cc_final: 0.8431 (mmt)
  outliers start: 12
  outliers final: 4
  residues processed: 60
  average time/residue: 0.5395
  time to fit residues: 33.4053
Evaluate side-chains
  53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  649 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.134348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.104213 restraints weight = 3723.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.53
r_work: 0.2968 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3892  Z= 0.143
  Angle     :  0.463   4.735   5279  Z= 0.245
  Chirality :  0.037   0.131    572
  Planarity :  0.003   0.033    645
  Dihedral  : 13.030 170.663    565
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  :  9.82 %
    Favored  : 86.05 %
  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:  3.59 (0.39), residues: 471
  helix:  2.99 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.59 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 624 
 TYR   0.010   0.001   TYR A 462 
 PHE   0.019   0.002   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.004   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3892)
  covalent geometry    : angle       0.46276 ( 5279)
  hydrogen bonds       : bond        0.05255 (  294)
  hydrogen bonds       : angle       3.60210 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8087 (tp30) cc_final: 0.7824 (mm-30)
REVERT: A  206 MET cc_start: 0.7146 (tpp) cc_final: 0.6039 (ttm)
REVERT: A  233 GLN cc_start: 0.8142 (tp40) cc_final: 0.7898 (tp40)
REVERT: A  253 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7830 (mp10)
REVERT: A  366 LYS cc_start: 0.8271 (mttm) cc_final: 0.7838 (mtmm)
REVERT: A  437 SER cc_start: 0.8645 (t) cc_final: 0.8188 (m)
REVERT: A  606 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7524 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 65
  average time/residue: 0.4960
  time to fit residues: 33.3444
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.135067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.105102 restraints weight = 3711.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.52
r_work: 0.2977 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3892  Z= 0.126
  Angle     :  0.442   4.884   5279  Z= 0.233
  Chirality :  0.036   0.125    572
  Planarity :  0.003   0.033    645
  Dihedral  : 12.467 171.558    565
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.14 %
    Favored  : 84.75 %
  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:  3.63 (0.39), residues: 471
  helix:  3.03 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.66 (0.62), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 163 
 TYR   0.010   0.001   TYR A 462 
 PHE   0.017   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3892)
  covalent geometry    : angle       0.44160 ( 5279)
  hydrogen bonds       : bond        0.04716 (  294)
  hydrogen bonds       : angle       3.52781 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8074 (tp30) cc_final: 0.7814 (mm-30)
REVERT: A  206 MET cc_start: 0.7216 (tpp) cc_final: 0.6790 (mmt)
REVERT: A  233 GLN cc_start: 0.8121 (tp40) cc_final: 0.7871 (tp40)
REVERT: A  253 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (mp10)
REVERT: A  366 LYS cc_start: 0.8200 (mttm) cc_final: 0.7804 (mppt)
REVERT: A  437 SER cc_start: 0.8630 (t) cc_final: 0.8199 (m)
REVERT: A  606 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7552 (mp)
  outliers start: 12
  outliers final: 5
  residues processed: 60
  average time/residue: 0.5649
  time to fit residues: 34.9810
Evaluate side-chains
  60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0270
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.134325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.104416 restraints weight = 3758.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.52
r_work: 0.2973 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3892  Z= 0.134
  Angle     :  0.453   4.928   5279  Z= 0.237
  Chirality :  0.037   0.127    572
  Planarity :  0.003   0.034    645
  Dihedral  : 12.158 171.336    565
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 11.37 %
    Favored  : 84.50 %
  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:  3.56 (0.38), residues: 471
  helix:  2.98 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.69 (0.61), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 624 
 TYR   0.009   0.001   TYR A 462 
 PHE   0.018   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.002   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3892)
  covalent geometry    : angle       0.45252 ( 5279)
  hydrogen bonds       : bond        0.04891 (  294)
  hydrogen bonds       : angle       3.54358 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8077 (tp30) cc_final: 0.7824 (mm-30)
REVERT: A  206 MET cc_start: 0.7251 (tpp) cc_final: 0.6162 (ttm)
REVERT: A  233 GLN cc_start: 0.8120 (tp40) cc_final: 0.7875 (tp40)
REVERT: A  366 LYS cc_start: 0.8246 (mttm) cc_final: 0.7900 (mppt)
REVERT: A  437 SER cc_start: 0.8622 (t) cc_final: 0.8250 (m)
REVERT: A  606 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7565 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 62
  average time/residue: 0.5107
  time to fit residues: 32.8016
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.134185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.104245 restraints weight = 3810.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.53
r_work: 0.2973 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3892  Z= 0.135
  Angle     :  0.464   4.965   5279  Z= 0.240
  Chirality :  0.037   0.127    572
  Planarity :  0.003   0.033    645
  Dihedral  : 11.929 170.898    565
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.66 %
    Favored  : 84.75 %
  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:  3.53 (0.38), residues: 471
  helix:  2.96 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.70 (0.61), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 228 
 TYR   0.009   0.001   TYR A 462 
 PHE   0.018   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3892)
  covalent geometry    : angle       0.46422 ( 5279)
  hydrogen bonds       : bond        0.04887 (  294)
  hydrogen bonds       : angle       3.54948 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8074 (tp30) cc_final: 0.7825 (mm-30)
REVERT: A  206 MET cc_start: 0.7336 (tpp) cc_final: 0.7030 (mmt)
REVERT: A  209 LEU cc_start: 0.7974 (tt) cc_final: 0.7583 (tt)
REVERT: A  233 GLN cc_start: 0.8086 (tp40) cc_final: 0.7846 (tp40)
REVERT: A  366 LYS cc_start: 0.8245 (mttm) cc_final: 0.7825 (mppt)
REVERT: A  437 SER cc_start: 0.8640 (t) cc_final: 0.8251 (m)
REVERT: A  606 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7595 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 53
  average time/residue: 0.5199
  time to fit residues: 28.5649
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.132907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.103151 restraints weight = 3791.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.53
r_work: 0.2954 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3892  Z= 0.153
  Angle     :  0.482   4.969   5279  Z= 0.249
  Chirality :  0.038   0.153    572
  Planarity :  0.003   0.033    645
  Dihedral  : 11.787 167.196    565
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.92 %
    Favored  : 84.24 %
  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:  3.36 (0.38), residues: 471
  helix:  2.84 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.75 (0.61), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 228 
 TYR   0.009   0.001   TYR A 169 
 PHE   0.020   0.002   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3892)
  covalent geometry    : angle       0.48223 ( 5279)
  hydrogen bonds       : bond        0.05262 (  294)
  hydrogen bonds       : angle       3.62912 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8081 (tp30) cc_final: 0.7559 (mm-30)
REVERT: A  150 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7875 (mp10)
REVERT: A  206 MET cc_start: 0.7174 (tpp) cc_final: 0.6921 (mmt)
REVERT: A  233 GLN cc_start: 0.8061 (tp40) cc_final: 0.7831 (tp40)
REVERT: A  366 LYS cc_start: 0.8292 (mttm) cc_final: 0.7845 (mppt)
REVERT: A  437 SER cc_start: 0.8666 (t) cc_final: 0.8262 (m)
REVERT: A  606 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7594 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 54
  average time/residue: 0.5593
  time to fit residues: 31.2523
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0070
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.133343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.103621 restraints weight = 3776.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.52
r_work: 0.2960 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3892  Z= 0.144
  Angle     :  0.478   5.586   5279  Z= 0.245
  Chirality :  0.038   0.197    572
  Planarity :  0.003   0.033    645
  Dihedral  : 11.713 168.713    565
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.18 %
    Favored  : 84.24 %
  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:  3.38 (0.38), residues: 471
  helix:  2.86 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.78 (0.61), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 624 
 TYR   0.009   0.001   TYR A 462 
 PHE   0.019   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3892)
  covalent geometry    : angle       0.47806 ( 5279)
  hydrogen bonds       : bond        0.05026 (  294)
  hydrogen bonds       : angle       3.61857 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8067 (tp30) cc_final: 0.7558 (mm-30)
REVERT: A  150 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7876 (mp10)
REVERT: A  206 MET cc_start: 0.7126 (tpp) cc_final: 0.6886 (mmt)
REVERT: A  209 LEU cc_start: 0.7964 (tt) cc_final: 0.7488 (tt)
REVERT: A  233 GLN cc_start: 0.8058 (tp40) cc_final: 0.7830 (tp40)
REVERT: A  366 LYS cc_start: 0.8249 (mttm) cc_final: 0.7844 (mppt)
REVERT: A  437 SER cc_start: 0.8665 (t) cc_final: 0.8258 (m)
REVERT: A  606 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7563 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 0.5293
  time to fit residues: 31.7731
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0770
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 667 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.133709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.103982 restraints weight = 3791.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.53
r_work: 0.2970 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3892  Z= 0.138
  Angle     :  0.477   5.370   5279  Z= 0.243
  Chirality :  0.038   0.197    572
  Planarity :  0.003   0.032    645
  Dihedral  : 11.656 170.376    565
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.95 %
    Favored  : 83.98 %
  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:  3.37 (0.38), residues: 471
  helix:  2.86 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.81 (0.62), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.009   0.001   TYR A 462 
 PHE   0.018   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.002   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3892)
  covalent geometry    : angle       0.47679 ( 5279)
  hydrogen bonds       : bond        0.04909 (  294)
  hydrogen bonds       : angle       3.62885 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.8063 (tp30) cc_final: 0.7529 (mm-30)
REVERT: A  150 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7858 (mp10)
REVERT: A  209 LEU cc_start: 0.7910 (tt) cc_final: 0.7324 (tt)
REVERT: A  233 GLN cc_start: 0.8040 (tp40) cc_final: 0.7765 (tp40)
REVERT: A  366 LYS cc_start: 0.8243 (mttm) cc_final: 0.7840 (mppt)
REVERT: A  437 SER cc_start: 0.8637 (t) cc_final: 0.8253 (m)
REVERT: A  606 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7574 (mp)
  outliers start: 8
  outliers final: 6
  residues processed: 57
  average time/residue: 0.4976
  time to fit residues: 29.4010
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.147213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.121485 restraints weight = 4097.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.40
r_work: 0.3407 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3892  Z= 0.161
  Angle     :  0.503   5.630   5279  Z= 0.256
  Chirality :  0.039   0.202    572
  Planarity :  0.003   0.033    645
  Dihedral  : 11.630 166.048    565
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.47 %
    Favored  : 83.20 %
  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:  3.24 (0.38), residues: 471
  helix:  2.78 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.87 (0.61), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 624 
 TYR   0.009   0.001   TYR A 169 
 PHE   0.021   0.002   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3892)
  covalent geometry    : angle       0.50258 ( 5279)
  hydrogen bonds       : bond        0.05358 (  294)
  hydrogen bonds       : angle       3.70283 (  876)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.7950 (tp30) cc_final: 0.7402 (mm-30)
REVERT: A  150 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7722 (mp10)
REVERT: A  209 LEU cc_start: 0.7953 (tt) cc_final: 0.7389 (tt)
REVERT: A  366 LYS cc_start: 0.8180 (mttm) cc_final: 0.7803 (mppt)
REVERT: A  437 SER cc_start: 0.8666 (t) cc_final: 0.8258 (m)
REVERT: A  606 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 57
  average time/residue: 0.5219
  time to fit residues: 30.7276
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  729 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.148066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.122541 restraints weight = 4077.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.39
r_work: 0.3416 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3892  Z= 0.145
  Angle     :  0.484   5.377   5279  Z= 0.248
  Chirality :  0.038   0.191    572
  Planarity :  0.003   0.033    645
  Dihedral  : 11.614 168.400    565
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.50 %
    Favored  : 82.43 %
  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:  3.28 (0.38), residues: 471
  helix:  2.81 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -0.92 (0.62), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 163 
 TYR   0.009   0.001   TYR A 462 
 PHE   0.019   0.001   PHE A 245 
 TRP   0.005   0.001   TRP A 333 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3892)
  covalent geometry    : angle       0.48446 ( 5279)
  hydrogen bonds       : bond        0.05030 (  294)
  hydrogen bonds       : angle       3.66217 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1531.34 seconds
wall clock time: 26 minutes 52.34 seconds (1612.34 seconds total)