Starting phenix.real_space_refine
on Fri Aug 22 14:26:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v3q_42950/08_2025/8v3q_42950.cif"
  }
  resolution = 3.1
  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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      22      5.16       5
     C    2556      2.51       5
     N     722      2.21       5
     O     729      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "M GLU    5": not complete - not flipped  Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4030
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 3971
          Classifications: {'peptide': 501}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 35, 'TRANS': 465}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "M"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 48
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'UNK:plan-1': 8, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.21, per 1000 atoms: 0.30
  Number of scatterers: 4030
  At special positions: 0
  Unit cell: (77.19, 73.455, 69.72, 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)
     Zn      1     29.99
     S      22     16.00
     O     729      8.00
     N     722      7.00
     C    2556      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 146.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 252 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 434 "


  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 4 sheets defined
      30.6% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 104
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 3.766A  pdb=" N   PHE A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 3.892A  pdb=" N   TYR A 315 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 340
    Processing helix  chain 'A' and resid 451 through 467
      removed outlier: 4.338A  pdb=" N   TYR A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      Proline residue:  A 462  - end of helix
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 494 through 497
      removed outlier: 3.559A  pdb=" N   GLY A 497 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 494 through 497'
    Processing helix  chain 'A' and resid 498 through 508
      removed outlier: 3.573A  pdb=" N   TYR A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 570
      removed outlier: 3.685A  pdb=" N   ALA A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ALA A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 601
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 3.635A  pdb=" N   ARG A 111 " --> pdb=" O   PHE A 152 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   THR A 112 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ARG A 118 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24
      removed outlier: 3.501A  pdb=" N   HIS A  21 " --> pdb=" O   TRP A  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 198
      removed outlier: 7.283A  pdb=" N   VAL A 205 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   SER A 212 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   PHE A 284 " --> pdb=" O   SER A 212 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ARG A 243 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   LYS A 287 " --> pdb=" O   ARG A 243 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   PHE A 245 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ILE A 289 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU A 247 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE A 244 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL A 431 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A 246 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LEU A 433 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 8.944A  pdb=" N   GLY A 435 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 220
      removed outlier: 3.714A  pdb=" N   ARG A 238 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    426 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: 0.82

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 642
        1.31 -     1.43: 1209
        1.43 -     1.56: 2249
        1.56 -     1.68: 7
        1.68 -     1.81: 33
  Bond restraints: 4140
  Sorted by residual:
  bond pdb=" C   GLU M   5 "
       pdb=" O   GLU M   5 "
    ideal  model  delta    sigma   weight residual
    1.231  1.181  0.050 2.00e-02 2.50e+03 6.26e+00
  bond pdb=" CB  VAL A 261 "
       pdb=" CG2 VAL A 261 "
    ideal  model  delta    sigma   weight residual
    1.521  1.441  0.080 3.30e-02 9.18e+02 5.89e+00
  bond pdb=" C   SER A 184 "
       pdb=" N   PRO A 185 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.71e+00
  bond pdb=" C   THR A 256 "
       pdb=" N   PRO A 257 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.28e-02 6.10e+03 4.60e+00
  bond pdb=" C   PHE A 546 "
       pdb=" N   PRO A 547 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.23e-02 6.61e+03 4.60e+00
  ... (remaining 4135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 5133
        1.94 -     3.88: 369
        3.88 -     5.82: 87
        5.82 -     7.76: 18
        7.76 -     9.70: 9
  Bond angle restraints: 5616
  Sorted by residual:
  angle pdb=" C   SER A 183 "
        pdb=" N   SER A 184 "
        pdb=" CA  SER A 184 "
      ideal   model   delta    sigma   weight residual
     120.51  129.21   -8.70 1.45e+00 4.76e-01 3.60e+01
  angle pdb=" C   LYS A 495 "
        pdb=" N   GLU A 496 "
        pdb=" CA  GLU A 496 "
      ideal   model   delta    sigma   weight residual
     120.82  128.43   -7.61 1.50e+00 4.44e-01 2.58e+01
  angle pdb=" CG  ARG A 549 "
        pdb=" CD  ARG A 549 "
        pdb=" NE  ARG A 549 "
      ideal   model   delta    sigma   weight residual
     112.00  120.77   -8.77 2.20e+00 2.07e-01 1.59e+01
  angle pdb=" N   THR A 256 "
        pdb=" CA  THR A 256 "
        pdb=" C   THR A 256 "
      ideal   model   delta    sigma   weight residual
     109.81  118.50   -8.69 2.21e+00 2.05e-01 1.55e+01
  angle pdb=" C   MET A 130 "
        pdb=" N   THR A 131 "
        pdb=" CA  THR A 131 "
      ideal   model   delta    sigma   weight residual
     120.82  126.56   -5.74 1.47e+00 4.63e-01 1.53e+01
  ... (remaining 5611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.43: 2315
       22.43 -    44.86: 127
       44.86 -    67.29: 18
       67.29 -    89.72: 3
       89.72 -   112.15: 1
  Dihedral angle restraints: 2464
    sinusoidal: 978
      harmonic: 1486
  Sorted by residual:
  dihedral pdb=" CB  GLU M   5 "
           pdb=" CG  GLU M   5 "
           pdb=" CD  GLU M   5 "
           pdb=" OE1 GLU M   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  112.15 -112.15     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" CA  MET A 444 "
           pdb=" C   MET A 444 "
           pdb=" N   TYR A 445 "
           pdb=" CA  TYR A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.05   17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR A 429 "
           pdb=" C   TYR A 429 "
           pdb=" N   TYR A 430 "
           pdb=" CA  TYR A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 2461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 483
       0.089 -    0.178: 93
       0.178 -    0.267: 14
       0.267 -    0.356: 1
       0.356 -    0.444: 2
  Chirality restraints: 593
  Sorted by residual:
  chirality pdb=" CB  VAL A  25 "
            pdb=" CA  VAL A  25 "
            pdb=" CG1 VAL A  25 "
            pdb=" CG2 VAL A  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CA  GLU M1001 "
            pdb=" N   GLU M1001 "
            pdb=" C   GLU M1001 "
            pdb=" CB  GLU M1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CB  VAL A 261 "
            pdb=" CA  VAL A 261 "
            pdb=" CG1 VAL A 261 "
            pdb=" CG2 VAL A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 590 not shown)

  Planarity restraints: 741
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 317 "   -0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   LYS A 317 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LYS A 317 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PRO A 318 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 258 "   -0.017 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   SER A 258 "    0.057 2.00e-02 2.50e+03
        pdb=" O   SER A 258 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER A 259 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 311 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.10e+00
        pdb=" C   LEU A 311 "    0.052 2.00e-02 2.50e+03
        pdb=" O   LEU A 311 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A 312 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 738 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 71
        2.67 -     3.23: 3511
        3.23 -     3.78: 6502
        3.78 -     4.34: 8749
        4.34 -     4.90: 14577
  Nonbonded interactions: 33410
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.109 2.230
  nonbonded pdb=" OE1 GLU M   5 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.111 2.230
  nonbonded pdb=" OE2 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.145 2.230
  nonbonded pdb=" O   HIS A 336 "
            pdb=" OG  SER A 340 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" OG  SER A 581 "
            pdb=" O   HIS A 583 "
     model   vdw
     2.399 3.040
  ... (remaining 33405 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 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:             8.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.040
  Find NCS groups from input model:        0.020
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
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      :  0.009   0.092   4143  Z= 0.407
  Angle     :  1.223   9.703   5616  Z= 0.680
  Chirality :  0.074   0.444    593
  Planarity :  0.010   0.059    741
  Dihedral  : 14.292 112.148   1504
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.34), residues: 493
  helix: -1.49 (0.34), residues: 140
  sheet:  0.93 (0.58), residues: 80
  loop : -1.04 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG A 549 
 TYR   0.030   0.004   TYR A 430 
 PHE   0.023   0.004   PHE A 262 
 TRP   0.017   0.003   TRP A 592 
 HIS   0.026   0.003   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00928 ( 4140)
  covalent geometry    : angle       1.22271 ( 5616)
  hydrogen bonds       : bond        0.17391 (  151)
  hydrogen bonds       : angle       7.79596 (  426)
  metal coordination   : bond        0.01221 (    2)
  Misc. bond           : bond        0.06001 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A    3 LEU cc_start: 0.7710 (mt) cc_final: 0.7418 (mp)
REVERT: A   13 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7749 (ttm170)
REVERT: A   69 ASN cc_start: 0.8022 (m-40) cc_final: 0.7817 (m110)
REVERT: A  118 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7685 (ttt90)
REVERT: A  120 GLU cc_start: 0.8158 (pt0) cc_final: 0.7580 (pt0)
REVERT: A  166 GLU cc_start: 0.7140 (tp30) cc_final: 0.6499 (tt0)
REVERT: A  169 ASN cc_start: 0.7551 (m-40) cc_final: 0.6882 (m-40)
REVERT: A  170 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6816 (mt0)
REVERT: A  172 ASP cc_start: 0.7329 (t0) cc_final: 0.7083 (t0)
REVERT: A  226 GLN cc_start: 0.8105 (tt0) cc_final: 0.7481 (tp-100)
REVERT: A  475 GLN cc_start: 0.8457 (mp10) cc_final: 0.8081 (mp10)
REVERT: A  481 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7552 (mm-30)
REVERT: A  595 LYS cc_start: 0.6603 (ttpt) cc_final: 0.5689 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1120
  time to fit residues: 8.6174
Evaluate side-chains
  47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0010
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    0.2980
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.0764

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

Flipped N/Q/H residues before XYZ refinement:
A 471 HIS
A 533 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.110350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.097736 restraints weight = 5625.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.63
r_work: 0.3008 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4143  Z= 0.112
  Angle     :  0.555   5.258   5616  Z= 0.290
  Chirality :  0.041   0.147    593
  Planarity :  0.005   0.041    741
  Dihedral  :  5.682  76.089    567
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.09 %
    Favored  : 88.73 %
  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: -0.11 (0.37), residues: 493
  helix:  0.35 (0.42), residues: 140
  sheet:  0.66 (0.56), residues: 90
  loop : -0.51 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 549 
 TYR   0.008   0.001   TYR A 102 
 PHE   0.012   0.001   PHE A 152 
 TRP   0.010   0.001   TRP A 592 
 HIS   0.009   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4140)
  covalent geometry    : angle       0.55492 ( 5616)
  hydrogen bonds       : bond        0.04178 (  151)
  hydrogen bonds       : angle       5.55435 (  426)
  metal coordination   : bond        0.00184 (    2)
  Misc. bond           : bond        0.00017 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.7986 (tp30) cc_final: 0.7601 (tt0)
REVERT: A  169 ASN cc_start: 0.7967 (m-40) cc_final: 0.7544 (m-40)
REVERT: A  190 TYR cc_start: 0.8663 (t80) cc_final: 0.8307 (t80)
REVERT: A  424 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7342 (tt0)
REVERT: A  595 LYS cc_start: 0.7692 (ttpt) cc_final: 0.6715 (mttt)
  outliers start: 5
  outliers final: 3
  residues processed: 56
  average time/residue: 0.1024
  time to fit residues: 6.8779
Evaluate side-chains
  40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  532 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 42 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0270
   chunk 35 optimal weight:    0.0040
   chunk 25 optimal weight:    0.0040
   chunk 39 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.0862

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.110486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.096747 restraints weight = 5605.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.80
r_work: 0.3007 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4143  Z= 0.101
  Angle     :  0.511   5.237   5616  Z= 0.263
  Chirality :  0.040   0.148    593
  Planarity :  0.004   0.038    741
  Dihedral  :  5.188  70.738    567
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.33 %
    Favored  : 87.79 %
  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 (0.39), residues: 493
  helix:  1.14 (0.44), residues: 140
  sheet:  0.63 (0.54), residues: 98
  loop : -0.24 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 549 
 TYR   0.009   0.001   TYR A 157 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.006   0.001   TRP A 592 
 HIS   0.005   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4140)
  covalent geometry    : angle       0.51068 ( 5616)
  hydrogen bonds       : bond        0.03393 (  151)
  hydrogen bonds       : angle       5.01434 (  426)
  metal coordination   : bond        0.00120 (    2)
  Misc. bond           : bond        0.00027 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  169 ASN cc_start: 0.7965 (m-40) cc_final: 0.7689 (m-40)
REVERT: A  190 TYR cc_start: 0.8691 (t80) cc_final: 0.8268 (t80)
REVERT: A  424 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7365 (tt0)
REVERT: A  459 MET cc_start: 0.9177 (mtm) cc_final: 0.8934 (mtm)
REVERT: A  569 MET cc_start: 0.8193 (mtp) cc_final: 0.7986 (mtp)
REVERT: A  595 LYS cc_start: 0.7676 (ttpt) cc_final: 0.6805 (mttt)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0834
  time to fit residues: 5.0709
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  532 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0470
   chunk 4 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0980
   chunk 44 optimal weight:    0.3980
   chunk 14 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.3278

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

Flipped N/Q/H residues before XYZ refinement:
A 336 HIS
A 533 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.103005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.089661 restraints weight = 5737.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.77
r_work: 0.2897 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4143  Z= 0.214
  Angle     :  0.596   5.415   5616  Z= 0.308
  Chirality :  0.044   0.181    593
  Planarity :  0.005   0.032    741
  Dihedral  :  5.554  71.981    567
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.03 %
    Favored  : 86.62 %
  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:  0.70 (0.39), residues: 493
  helix:  1.38 (0.46), residues: 140
  sheet:  1.35 (0.62), residues: 82
  loop : -0.28 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 549 
 TYR   0.020   0.002   TYR A 102 
 PHE   0.012   0.002   PHE A 143 
 TRP   0.006   0.001   TRP A 592 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 4140)
  covalent geometry    : angle       0.59645 ( 5616)
  hydrogen bonds       : bond        0.04213 (  151)
  hydrogen bonds       : angle       5.15212 (  426)
  metal coordination   : bond        0.00592 (    2)
  Misc. bond           : bond        0.00114 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.8852 (p90) cc_final: 0.8489 (p90)
REVERT: A  169 ASN cc_start: 0.7965 (m-40) cc_final: 0.7713 (m-40)
REVERT: A  424 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7332 (tt0)
REVERT: A  496 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (tm-30)
REVERT: A  595 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7382 (tppt)
  outliers start: 10
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0808
  time to fit residues: 4.6247
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  496 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0170
   chunk 6 optimal weight:    0.2980
   chunk 44 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.1996

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
A 533 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.104398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.091058 restraints weight = 5716.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.76
r_work: 0.2919 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4143  Z= 0.145
  Angle     :  0.533   5.265   5616  Z= 0.273
  Chirality :  0.041   0.161    593
  Planarity :  0.004   0.033    741
  Dihedral  :  5.403  74.154    567
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.27 %
    Favored  : 87.09 %
  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:  0.74 (0.39), residues: 493
  helix:  1.55 (0.45), residues: 140
  sheet:  1.25 (0.61), residues: 82
  loop : -0.29 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 549 
 TYR   0.013   0.002   TYR A 102 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.007   0.001   TRP A 592 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4140)
  covalent geometry    : angle       0.53327 ( 5616)
  hydrogen bonds       : bond        0.03534 (  151)
  hydrogen bonds       : angle       4.97522 (  426)
  metal coordination   : bond        0.00321 (    2)
  Misc. bond           : bond        0.00065 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7546 (mtm180)
REVERT: A  128 PHE cc_start: 0.8849 (p90) cc_final: 0.8469 (p90)
REVERT: A  169 ASN cc_start: 0.7892 (m-40) cc_final: 0.7665 (m-40)
REVERT: A  424 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7388 (tt0)
REVERT: A  459 MET cc_start: 0.9213 (mtm) cc_final: 0.9010 (mtm)
REVERT: A  595 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7412 (tppt)
  outliers start: 7
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0858
  time to fit residues: 4.6064
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.0070
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0970
   chunk 7 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 32 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.1194

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.105876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.092383 restraints weight = 5737.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.78
r_work: 0.2931 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4143  Z= 0.109
  Angle     :  0.508   5.243   5616  Z= 0.259
  Chirality :  0.040   0.155    593
  Planarity :  0.004   0.032    741
  Dihedral  :  5.163  72.402    567
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.21 %
    Favored  : 85.92 %
  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:  0.86 (0.39), residues: 493
  helix:  1.76 (0.45), residues: 140
  sheet:  0.97 (0.58), residues: 88
  loop : -0.18 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 549 
 TYR   0.009   0.001   TYR A 102 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.008   0.001   TRP A 592 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4140)
  covalent geometry    : angle       0.50824 ( 5616)
  hydrogen bonds       : bond        0.03208 (  151)
  hydrogen bonds       : angle       4.79949 (  426)
  metal coordination   : bond        0.00198 (    2)
  Misc. bond           : bond        0.00045 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7484 (mtm180)
REVERT: A  128 PHE cc_start: 0.8831 (p90) cc_final: 0.8453 (p90)
REVERT: A  169 ASN cc_start: 0.7891 (m-40) cc_final: 0.7666 (m-40)
REVERT: A  424 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7370 (tt0)
REVERT: A  459 MET cc_start: 0.9145 (mtm) cc_final: 0.8900 (mtm)
REVERT: A  549 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.8006 (mtt-85)
REVERT: A  595 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7462 (tppt)
  outliers start: 8
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0946
  time to fit residues: 4.9533
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  569 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 24 optimal weight:    0.0670
   chunk 14 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0980
   chunk 46 optimal weight:    0.2980
   chunk 32 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.1718

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.110097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.095816 restraints weight = 5606.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.87
r_work: 0.3006 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4143  Z= 0.132
  Angle     :  0.525   6.024   5616  Z= 0.267
  Chirality :  0.041   0.163    593
  Planarity :  0.004   0.032    741
  Dihedral  :  5.114  70.631    567
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.27 %
    Favored  : 86.62 %
  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:  0.83 (0.39), residues: 493
  helix:  1.80 (0.45), residues: 140
  sheet:  0.84 (0.58), residues: 88
  loop : -0.19 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 549 
 TYR   0.011   0.001   TYR A 102 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.008   0.001   TRP A 592 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4140)
  covalent geometry    : angle       0.52459 ( 5616)
  hydrogen bonds       : bond        0.03322 (  151)
  hydrogen bonds       : angle       4.79304 (  426)
  metal coordination   : bond        0.00262 (    2)
  Misc. bond           : bond        0.00066 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7528 (mtm180)
REVERT: A  128 PHE cc_start: 0.8866 (p90) cc_final: 0.8497 (p90)
REVERT: A  169 ASN cc_start: 0.8012 (m-40) cc_final: 0.7792 (m-40)
REVERT: A  424 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7424 (tt0)
REVERT: A  459 MET cc_start: 0.9158 (mtm) cc_final: 0.8957 (mtm)
REVERT: A  549 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8050 (mtt-85)
REVERT: A  595 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7546 (tppt)
  outliers start: 9
  outliers final: 6
  residues processed: 42
  average time/residue: 0.1041
  time to fit residues: 5.2129
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  569 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0060
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0070
   chunk 40 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.1792

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.110656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.096581 restraints weight = 5507.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.89
r_work: 0.3000 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4143  Z= 0.133
  Angle     :  0.523   6.444   5616  Z= 0.266
  Chirality :  0.041   0.172    593
  Planarity :  0.004   0.034    741
  Dihedral  :  5.070  69.097    567
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.74 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.84 (0.39), residues: 493
  helix:  1.79 (0.45), residues: 140
  sheet:  0.85 (0.58), residues: 88
  loop : -0.18 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 549 
 TYR   0.012   0.001   TYR A 102 
 PHE   0.008   0.001   PHE A 265 
 TRP   0.007   0.001   TRP A 592 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4140)
  covalent geometry    : angle       0.52272 ( 5616)
  hydrogen bonds       : bond        0.03326 (  151)
  hydrogen bonds       : angle       4.78579 (  426)
  metal coordination   : bond        0.00279 (    2)
  Misc. bond           : bond        0.00069 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7432 (mtm180)
REVERT: A  128 PHE cc_start: 0.8905 (p90) cc_final: 0.8522 (p90)
REVERT: A  169 ASN cc_start: 0.7987 (m-40) cc_final: 0.7726 (m-40)
REVERT: A  424 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7489 (tt0)
REVERT: A  549 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8033 (mtt-85)
REVERT: A  595 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7453 (tppt)
  outliers start: 8
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0941
  time to fit residues: 4.5755
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  569 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0470
   chunk 47 optimal weight:    0.1980
   chunk 26 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0980
   chunk 12 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0980
   chunk 27 optimal weight:    0.1980
   chunk 16 optimal weight:    0.2980
   chunk 36 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0870
   overall best weight:    0.1056

-------------------------------------------------------------------------------
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 = 0.3338 r_free = 0.3338 target = 0.112228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.098302 restraints weight = 5588.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.84
r_work: 0.3028 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4143  Z= 0.104
  Angle     :  0.504   6.317   5616  Z= 0.255
  Chirality :  0.040   0.159    593
  Planarity :  0.004   0.034    741
  Dihedral  :  4.881  66.873    567
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.21 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.90 (0.40), residues: 493
  helix:  1.90 (0.45), residues: 140
  sheet:  0.82 (0.58), residues: 88
  loop : -0.15 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 549 
 TYR   0.009   0.001   TYR A 157 
 PHE   0.009   0.001   PHE A 265 
 TRP   0.010   0.001   TRP A 592 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4140)
  covalent geometry    : angle       0.50361 ( 5616)
  hydrogen bonds       : bond        0.03056 (  151)
  hydrogen bonds       : angle       4.68033 (  426)
  metal coordination   : bond        0.00173 (    2)
  Misc. bond           : bond        0.00042 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  116 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7444 (mtm180)
REVERT: A  128 PHE cc_start: 0.8834 (p90) cc_final: 0.8475 (p90)
REVERT: A  169 ASN cc_start: 0.8011 (m-40) cc_final: 0.7794 (m-40)
REVERT: A  424 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7508 (tt0)
REVERT: A  459 MET cc_start: 0.8826 (mtm) cc_final: 0.8558 (mtm)
REVERT: A  549 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7963 (mtt-85)
REVERT: A  595 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7552 (tppt)
  outliers start: 6
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1098
  time to fit residues: 5.2527
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  424 GLU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  569 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 44 optimal weight:    0.4980
   chunk 2 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0000
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0770
   chunk 14 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0570
   overall best weight:    0.0636

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.114845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100224 restraints weight = 5456.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.96
r_work: 0.3054 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4143  Z= 0.091
  Angle     :  0.491   6.225   5616  Z= 0.247
  Chirality :  0.040   0.177    593
  Planarity :  0.004   0.036    741
  Dihedral  :  4.517  59.737    567
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.21 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.87 (0.40), residues: 493
  helix:  2.03 (0.45), residues: 140
  sheet:  0.45 (0.55), residues: 98
  loop : -0.14 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 601 
 TYR   0.009   0.001   TYR A 157 
 PHE   0.010   0.001   PHE A 265 
 TRP   0.015   0.001   TRP A 592 
 HIS   0.005   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4140)
  covalent geometry    : angle       0.49050 ( 5616)
  hydrogen bonds       : bond        0.02749 (  151)
  hydrogen bonds       : angle       4.52986 (  426)
  metal coordination   : bond        0.00101 (    2)
  Misc. bond           : bond        0.00026 (    1)

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

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

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  986 Ramachandran restraints generated.
    493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  106 MET cc_start: 0.8550 (tpt) cc_final: 0.8275 (tpt)
REVERT: A  169 ASN cc_start: 0.8017 (m-40) cc_final: 0.7759 (m-40)
REVERT: A  190 TYR cc_start: 0.8879 (t80) cc_final: 0.8565 (t80)
REVERT: A  424 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7531 (tt0)
REVERT: A  459 MET cc_start: 0.8621 (mtm) cc_final: 0.8408 (mtm)
REVERT: A  549 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7938 (mtt-85)
REVERT: A  595 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7339 (tppt)
  outliers start: 6
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0775
  time to fit residues: 4.4626
Evaluate side-chains
  42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  569 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0040
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.2792

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.108549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.094032 restraints weight = 5549.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.87
r_work: 0.2984 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4143  Z= 0.186
  Angle     :  0.575  10.643   5616  Z= 0.290
  Chirality :  0.043   0.179    593
  Planarity :  0.004   0.033    741
  Dihedral  :  4.728  53.230    567
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.91 %
    Favored  : 85.45 %
  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:  0.81 (0.39), residues: 493
  helix:  1.78 (0.45), residues: 139
  sheet:  0.81 (0.59), residues: 90
  loop : -0.19 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 601 
 TYR   0.017   0.002   TYR A 102 
 PHE   0.010   0.002   PHE A 128 
 TRP   0.014   0.001   TRP A 592 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 4140)
  covalent geometry    : angle       0.57469 ( 5616)
  hydrogen bonds       : bond        0.03664 (  151)
  hydrogen bonds       : angle       4.91162 (  426)
  metal coordination   : bond        0.00437 (    2)
  Misc. bond           : bond        0.00118 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1232.96 seconds
wall clock time: 21 minutes 52.73 seconds (1312.73 seconds total)