Starting phenix.real_space_refine
on Tue Mar  3 18:26:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2026/7kdt_22829.cif"
  }
  resolution = 3.05
  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=   0.105
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
     S      27      5.16       5
     C    2543      2.51       5
     N     683      2.21       5
     O     769      1.98       5
     H    4042      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8064
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 7444
          Classifications: {'peptide': 467}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 454}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 620
          Classifications: {'peptide': 38}
          Link IDs: {'PTRANS': 3, 'TRANS': 34}
  Time building chain proxies: 1.28, per 1000 atoms: 0.16
  Number of scatterers: 8064
  At special positions: 0
  Unit cell: (57.546, 70.89, 115.926, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     O     769      8.00
     N     683      7.00
     C    2543      6.00
     H    4042      1.00
    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: 0.68
  Conformation dependent library (CDL) restraints added in 114.0 milliseconds
  

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  976

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      85.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 127
      removed outlier: 4.286A  pdb=" N   ALA A 114 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 124 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 145 through 149
    Processing helix  chain 'A' and resid 152 through 166
      removed outlier: 3.708A  pdb=" N   ALA A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE A 163 " --> pdb=" O   ARG A 159 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 183
    Processing helix  chain 'A' and resid 186 through 200
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 221 through 245
      removed outlier: 3.571A  pdb=" N   GLU A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 262
    Processing helix  chain 'A' and resid 299 through 307
      removed outlier: 4.360A  pdb=" N   GLN A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   TYR A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 311
      No H-bonds generated for 'chain 'A' and resid 309 through 311'
    Processing helix  chain 'A' and resid 312 through 321
      removed outlier: 3.501A  pdb=" N   LYS A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 343
      removed outlier: 6.115A  pdb=" N   GLU A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   LEU A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 358
      Proline residue:  A 350  - end of helix
      removed outlier: 3.595A  pdb=" N   VAL A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 380
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 3.624A  pdb=" N   ALA A 394 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 414
      removed outlier: 3.809A  pdb=" N   TYR A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.521A  pdb=" N   ALA A 420 " --> pdb=" O   GLN A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 452
      removed outlier: 3.653A  pdb=" N   GLN A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 472
      removed outlier: 3.816A  pdb=" N   GLU A 466 " --> pdb=" O   MET A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 489
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.514A  pdb=" N   GLU A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 521
      removed outlier: 4.136A  pdb=" N   TYR A 513 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 541
      removed outlier: 3.881A  pdb=" N   GLU A 532 " --> pdb=" O   ASP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 558
    Processing helix  chain 'A' and resid 560 through 573
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 3.688A  pdb=" N   HIS A 583 " --> pdb=" O   MET A 579 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 587 " --> pdb=" O   HIS A 583 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A 599 " --> pdb=" O   THR A 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 69
      removed outlier: 4.876A  pdb=" N   SER B  63 " --> pdb=" O   LYS B  59 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B  64 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   PHE B  69 " --> pdb=" O   GLU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 76

    290 hydrogen bonds defined for protein.
    858 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: 1.36

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        0.86 -     1.06: 1022
        1.06 -     1.25: 3587
        1.25 -     1.44: 1110
        1.44 -     1.63: 2367
        1.63 -     1.82: 42
  Bond restraints: 8128
  Sorted by residual:
  bond pdb=" C   GLN A 115 "
       pdb=" O   GLN A 115 "
    ideal  model  delta    sigma   weight residual
    1.236  1.141  0.095 1.15e-02 7.56e+03 6.85e+01
  bond pdb=" N   GLU A 549 "
       pdb=" H   GLU A 549 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" CD1 TYR A 479 "
       pdb=" HD1 TYR A 479 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" CD1 PHE A 390 "
       pdb=" HD1 PHE A 390 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" CD1 TYR A 304 "
       pdb=" HD1 TYR A 304 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.62e+01
  ... (remaining 8123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 12596
        2.65 -     5.29: 1638
        5.29 -     7.94: 467
        7.94 -    10.58: 19
       10.58 -    13.23: 10
  Bond angle restraints: 14730
  Sorted by residual:
  angle pdb=" CA  GLN A 115 "
        pdb=" C   GLN A 115 "
        pdb=" O   GLN A 115 "
      ideal   model   delta    sigma   weight residual
     120.82  114.53    6.29 1.05e+00 9.07e-01 3.58e+01
  angle pdb=" CA  GLN A 132 "
        pdb=" C   GLN A 132 "
        pdb=" O   GLN A 132 "
      ideal   model   delta    sigma   weight residual
     120.42  114.45    5.97 1.06e+00 8.90e-01 3.18e+01
  angle pdb=" N   GLN A 416 "
        pdb=" CA  GLN A 416 "
        pdb=" C   GLN A 416 "
      ideal   model   delta    sigma   weight residual
     109.62  102.09    7.53 1.50e+00 4.44e-01 2.52e+01
  angle pdb=" C   LYS A 516 "
        pdb=" N   GLY A 517 "
        pdb=" CA  GLY A 517 "
      ideal   model   delta    sigma   weight residual
     119.94  125.39   -5.45 1.09e+00 8.42e-01 2.50e+01
  angle pdb=" CA  LYS A 349 "
        pdb=" C   LYS A 349 "
        pdb=" O   LYS A 349 "
      ideal   model   delta    sigma   weight residual
     118.33  113.80    4.53 9.20e-01 1.18e+00 2.43e+01
  ... (remaining 14725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3508
       17.70 -    35.41: 182
       35.41 -    53.11: 47
       53.11 -    70.81: 47
       70.81 -    88.52: 21
  Dihedral angle restraints: 3805
    sinusoidal: 2092
      harmonic: 1713
  Sorted by residual:
  dihedral pdb=" CA  GLU A 320 "
           pdb=" C   GLU A 320 "
           pdb=" N   ILE A 321 "
           pdb=" CA  ILE A 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.67   28.33     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   ARG B  47 "
           pdb=" CA  ARG B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.02   27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  THR A 451 "
           pdb=" C   THR A 451 "
           pdb=" N   GLY A 452 "
           pdb=" CA  GLY A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 3802 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 342
       0.063 -    0.127: 181
       0.127 -    0.190: 51
       0.190 -    0.253: 22
       0.253 -    0.316: 6
  Chirality restraints: 602
  Sorted by residual:
  chirality pdb=" CA  GLU A 308 "
            pdb=" N   GLU A 308 "
            pdb=" C   GLU A 308 "
            pdb=" CB  GLU A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  PHE A 219 "
            pdb=" N   PHE A 219 "
            pdb=" C   PHE A 219 "
            pdb=" CB  PHE A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ARG A 529 "
            pdb=" N   ARG A 529 "
            pdb=" C   ARG A 529 "
            pdb=" CB  ARG A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 599 not shown)

  Planarity restraints: 1201
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 520 "    0.056 2.00e-02 2.50e+03   4.40e-01 2.91e+03
        pdb=" CD  GLN A 520 "   -0.018 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 520 "   -0.052 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 520 "    0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN A 520 "    0.768 2.00e-02 2.50e+03
        pdb="HE22 GLN A 520 "   -0.754 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 115 "    0.078 2.00e-02 2.50e+03   4.36e-01 2.85e+03
        pdb=" CD  GLN A 115 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 115 "   -0.084 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 115 "    0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN A 115 "   -0.753 2.00e-02 2.50e+03
        pdb="HE22 GLN A 115 "    0.748 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 220 "    0.119 2.00e-02 2.50e+03   4.33e-01 2.82e+03
        pdb=" CD  GLN A 220 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 220 "   -0.115 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 220 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A 220 "    0.745 2.00e-02 2.50e+03
        pdb="HE22 GLN A 220 "   -0.738 2.00e-02 2.50e+03
  ... (remaining 1198 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 413
        2.20 -     2.80: 15423
        2.80 -     3.40: 23181
        3.40 -     4.00: 29503
        4.00 -     4.60: 44103
  Nonbonded interactions: 112623
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 267 "
            pdb=" HG  SER A 270 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU A 217 "
            pdb=" HG  SER A 224 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" OD1 ASP A 151 "
            pdb=" HG  SER A 153 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" O   ALA A 483 "
            pdb=" HG1 THR A 487 "
     model   vdw
     1.654 2.450
  nonbonded pdb=" OD1 ASN A 509 "
            pdb=" HG1 THR A 512 "
     model   vdw
     1.663 2.450
  ... (remaining 112618 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:             1.300
  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:             0.030
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
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      :  0.012   0.095   4086  Z= 0.757
  Angle     :  1.742   7.528   5493  Z= 1.206
  Chirality :  0.088   0.316    602
  Planarity :  0.018   0.193    714
  Dihedral  : 14.556  88.516   1574
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 0.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.17 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.32), residues: 499
  helix: -0.92 (0.21), residues: 405
  sheet:  None (None), residues: 0
  loop : -0.95 (0.65), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG A 247 
 TYR   0.171   0.021   TYR A 186 
 PHE   0.070   0.015   PHE A 191 
 TRP   0.059   0.018   TRP A 523 
 HIS   0.012   0.004   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.01225 ( 4086)
  covalent geometry    : angle       1.74199 ( 5493)
  hydrogen bonds       : bond        0.21367 (  290)
  hydrogen bonds       : angle       7.09262 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 LYS cc_start: 0.8506 (tttp) cc_final: 0.8177 (mtpt)
  outliers start: 2
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2048
  time to fit residues: 29.7347
Evaluate side-chains
  72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 409 GLN
A 515 HIS
A 520 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127420 restraints weight = 16003.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.54
r_work: 0.3562 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4086  Z= 0.146
  Angle     :  0.601   5.444   5493  Z= 0.331
  Chirality :  0.035   0.134    602
  Planarity :  0.005   0.056    714
  Dihedral  :  4.969  23.870    542
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  6.76 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.36), residues: 499
  helix:  0.96 (0.24), residues: 413
  sheet:  None (None), residues: 0
  loop : -0.75 (0.61), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 529 
 TYR   0.023   0.002   TYR A 186 
 PHE   0.021   0.002   PHE A 338 
 TRP   0.009   0.002   TRP A 169 
 HIS   0.004   0.002   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4086)
  covalent geometry    : angle       0.60150 ( 5493)
  hydrogen bonds       : bond        0.05388 (  290)
  hydrogen bonds       : angle       4.20592 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8026 (tm-30)
REVERT: A  392 MET cc_start: 0.7676 (mmp) cc_final: 0.7364 (tpt)
REVERT: A  425 ASP cc_start: 0.8443 (t0) cc_final: 0.8127 (m-30)
REVERT: A  462 MET cc_start: 0.7199 (mmt) cc_final: 0.6919 (mmt)
REVERT: A  531 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7682 (tt)
REVERT: B   59 LYS cc_start: 0.8220 (tttp) cc_final: 0.8009 (mtpt)
  outliers start: 4
  outliers final: 2
  residues processed: 82
  average time/residue: 0.1447
  time to fit residues: 14.9569
Evaluate side-chains
  72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0470
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7680

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.152860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.126980 restraints weight = 16177.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.75
r_work: 0.3550 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4086  Z= 0.118
  Angle     :  0.512   4.166   5493  Z= 0.277
  Chirality :  0.033   0.118    602
  Planarity :  0.003   0.047    714
  Dihedral  :  4.385  20.742    542
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  6.76 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.37), residues: 499
  helix:  1.60 (0.25), residues: 415
  sheet:  None (None), residues: 0
  loop : -0.34 (0.67), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 529 
 TYR   0.013   0.001   TYR A 186 
 PHE   0.020   0.002   PHE A 163 
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4086)
  covalent geometry    : angle       0.51217 ( 5493)
  hydrogen bonds       : bond        0.04316 (  290)
  hydrogen bonds       : angle       3.79029 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 ASN cc_start: 0.7720 (m-40) cc_final: 0.7288 (p0)
REVERT: A  425 ASP cc_start: 0.8302 (t0) cc_final: 0.8084 (m-30)
REVERT: A  450 TYR cc_start: 0.8257 (t80) cc_final: 0.7934 (t80)
REVERT: A  462 MET cc_start: 0.7053 (mmt) cc_final: 0.6752 (mmt)
  outliers start: 5
  outliers final: 3
  residues processed: 76
  average time/residue: 0.1694
  time to fit residues: 15.9786
Evaluate side-chains
  65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 40 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.152387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.126850 restraints weight = 16320.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.62
r_work: 0.3559 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4086  Z= 0.106
  Angle     :  0.471   4.716   5493  Z= 0.252
  Chirality :  0.032   0.115    602
  Planarity :  0.003   0.042    714
  Dihedral  :  4.083  19.339    542
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.69 %
    Favored  : 91.38 %
  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 are not related in a simple way.
  whole:  2.39 (0.38), residues: 499
  helix:  1.96 (0.25), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.25 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 159 
 TYR   0.010   0.001   TYR A 298 
 PHE   0.013   0.001   PHE A 338 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 4086)
  covalent geometry    : angle       0.47070 ( 5493)
  hydrogen bonds       : bond        0.03760 (  290)
  hydrogen bonds       : angle       3.57243 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8211 (mm-30)
REVERT: A  271 GLN cc_start: 0.7275 (mt0) cc_final: 0.7026 (mt0)
REVERT: A  425 ASP cc_start: 0.8556 (t0) cc_final: 0.8319 (m-30)
REVERT: A  450 TYR cc_start: 0.8289 (t80) cc_final: 0.7930 (t80)
  outliers start: 4
  outliers final: 1
  residues processed: 69
  average time/residue: 0.1585
  time to fit residues: 13.7266
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.149873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.124047 restraints weight = 16306.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.69
r_work: 0.3514 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.5045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4086  Z= 0.129
  Angle     :  0.470   4.191   5493  Z= 0.257
  Chirality :  0.033   0.120    602
  Planarity :  0.003   0.039    714
  Dihedral  :  4.029  18.444    542
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.62 %
    Favored  : 90.68 %
  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:  2.43 (0.38), residues: 499
  helix:  1.99 (0.25), residues: 417
  sheet:  None (None), residues: 0
  loop : -0.33 (0.72), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 407 
 TYR   0.010   0.001   TYR A 377 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.003   0.002   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4086)
  covalent geometry    : angle       0.46997 ( 5493)
  hydrogen bonds       : bond        0.04044 (  290)
  hydrogen bonds       : angle       3.65326 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8213 (mm-30)
REVERT: A  425 ASP cc_start: 0.8427 (t0) cc_final: 0.8149 (m-30)
REVERT: A  450 TYR cc_start: 0.8265 (t80) cc_final: 0.7862 (t80)
  outliers start: 3
  outliers final: 3
  residues processed: 63
  average time/residue: 0.1234
  time to fit residues: 10.1295
Evaluate side-chains
  63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.149502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.123735 restraints weight = 16285.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.67
r_work: 0.3505 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4086  Z= 0.132
  Angle     :  0.474   4.254   5493  Z= 0.257
  Chirality :  0.033   0.117    602
  Planarity :  0.003   0.042    714
  Dihedral  :  3.977  17.909    542
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.09 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.37), residues: 499
  helix:  2.04 (0.25), residues: 417
  sheet:  None (None), residues: 0
  loop : -0.27 (0.74), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 407 
 TYR   0.010   0.001   TYR A 377 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.007   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4086)
  covalent geometry    : angle       0.47360 ( 5493)
  hydrogen bonds       : bond        0.03984 (  290)
  hydrogen bonds       : angle       3.63482 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8203 (mm-30)
REVERT: A  246 ASN cc_start: 0.8856 (m-40) cc_final: 0.8581 (t0)
REVERT: A  425 ASP cc_start: 0.8614 (t0) cc_final: 0.8323 (m-30)
REVERT: A  450 TYR cc_start: 0.8304 (t80) cc_final: 0.7903 (t80)
  outliers start: 3
  outliers final: 3
  residues processed: 64
  average time/residue: 0.1381
  time to fit residues: 11.2979
Evaluate side-chains
  63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.148523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122541 restraints weight = 16410.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.69
r_work: 0.3485 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.5271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4086  Z= 0.146
  Angle     :  0.489   4.462   5493  Z= 0.267
  Chirality :  0.033   0.119    602
  Planarity :  0.003   0.040    714
  Dihedral  :  4.000  17.503    542
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.86 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.37), residues: 499
  helix:  2.10 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.55 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 407 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.002   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4086)
  covalent geometry    : angle       0.48859 ( 5493)
  hydrogen bonds       : bond        0.04095 (  290)
  hydrogen bonds       : angle       3.68022 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8181 (mm-30)
REVERT: A  158 ASN cc_start: 0.8574 (m-40) cc_final: 0.8283 (m-40)
REVERT: A  246 ASN cc_start: 0.8880 (m-40) cc_final: 0.8605 (t0)
REVERT: A  425 ASP cc_start: 0.8595 (t0) cc_final: 0.8307 (m-30)
REVERT: A  450 TYR cc_start: 0.8296 (t80) cc_final: 0.7909 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1510
  time to fit residues: 12.6231
Evaluate side-chains
  62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.150041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124312 restraints weight = 16448.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.69
r_work: 0.3513 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4086  Z= 0.113
  Angle     :  0.460   4.221   5493  Z= 0.248
  Chirality :  0.032   0.113    602
  Planarity :  0.003   0.042    714
  Dihedral  :  3.881  17.211    542
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.09 %
    Favored  : 89.98 %
  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:  2.81 (0.37), residues: 499
  helix:  2.34 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.53 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 529 
 TYR   0.008   0.001   TYR A 482 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4086)
  covalent geometry    : angle       0.45998 ( 5493)
  hydrogen bonds       : bond        0.03641 (  290)
  hydrogen bonds       : angle       3.48177 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8189 (mm-30)
REVERT: A  158 ASN cc_start: 0.8589 (m-40) cc_final: 0.8296 (m-40)
REVERT: A  167 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7677 (mp10)
REVERT: A  246 ASN cc_start: 0.8851 (m-40) cc_final: 0.8640 (t0)
REVERT: A  410 LEU cc_start: 0.8663 (tp) cc_final: 0.8462 (tp)
REVERT: A  425 ASP cc_start: 0.8584 (t0) cc_final: 0.8303 (m-30)
REVERT: A  450 TYR cc_start: 0.8278 (t80) cc_final: 0.7861 (t80)
REVERT: A  462 MET cc_start: 0.7533 (mmm) cc_final: 0.7219 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1806
  time to fit residues: 15.0688
Evaluate side-chains
  65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLN
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.148391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.122596 restraints weight = 16427.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.68
r_work: 0.3490 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4086  Z= 0.135
  Angle     :  0.472   4.340   5493  Z= 0.256
  Chirality :  0.033   0.117    602
  Planarity :  0.003   0.039    714
  Dihedral  :  3.915  17.269    542
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.09 %
    Favored  : 89.74 %
  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:  2.76 (0.37), residues: 499
  helix:  2.30 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.53 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 407 
 TYR   0.011   0.001   TYR A 377 
 PHE   0.013   0.001   PHE A 338 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4086)
  covalent geometry    : angle       0.47217 ( 5493)
  hydrogen bonds       : bond        0.03937 (  290)
  hydrogen bonds       : angle       3.58563 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8158 (mm-30)
REVERT: A  158 ASN cc_start: 0.8592 (m-40) cc_final: 0.8287 (m-40)
REVERT: A  167 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7702 (mp10)
REVERT: A  425 ASP cc_start: 0.8570 (t0) cc_final: 0.8276 (m-30)
REVERT: A  450 TYR cc_start: 0.8299 (t80) cc_final: 0.7928 (t80)
REVERT: A  551 MET cc_start: 0.8181 (ttp) cc_final: 0.7846 (tpp)
REVERT: A  561 MET cc_start: 0.7856 (mmt) cc_final: 0.6023 (mmt)
  outliers start: 5
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1438
  time to fit residues: 11.7316
Evaluate side-chains
  64 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLN
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.150606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125070 restraints weight = 16308.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.68
r_work: 0.3526 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4086  Z= 0.105
  Angle     :  0.450   4.301   5493  Z= 0.242
  Chirality :  0.032   0.112    602
  Planarity :  0.003   0.041    714
  Dihedral  :  3.797  16.732    542
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.56 %
    Favored  : 89.51 %
  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:  3.04 (0.37), residues: 499
  helix:  2.50 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.48 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 529 
 TYR   0.007   0.001   TYR A 377 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 4086)
  covalent geometry    : angle       0.44997 ( 5493)
  hydrogen bonds       : bond        0.03497 (  290)
  hydrogen bonds       : angle       3.41321 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8168 (mm-30)
REVERT: A  158 ASN cc_start: 0.8551 (m-40) cc_final: 0.8249 (m-40)
REVERT: A  167 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7713 (mp10)
REVERT: A  425 ASP cc_start: 0.8414 (t0) cc_final: 0.8133 (m-30)
REVERT: A  450 TYR cc_start: 0.8285 (t80) cc_final: 0.7869 (t80)
REVERT: A  462 MET cc_start: 0.7472 (mmm) cc_final: 0.7237 (mmt)
REVERT: A  561 MET cc_start: 0.7644 (mmt) cc_final: 0.5843 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 66
  average time/residue: 0.1582
  time to fit residues: 13.1780
Evaluate side-chains
  62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain B residue   60 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.147924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122112 restraints weight = 16328.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.69
r_work: 0.3489 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4086  Z= 0.153
  Angle     :  0.483   4.343   5493  Z= 0.263
  Chirality :  0.033   0.119    602
  Planarity :  0.003   0.040    714
  Dihedral  :  3.915  15.751    542
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.56 %
    Favored  : 89.74 %
  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:  2.73 (0.37), residues: 499
  helix:  2.29 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.55 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 407 
 TYR   0.011   0.001   TYR A 377 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.002   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4086)
  covalent geometry    : angle       0.48258 ( 5493)
  hydrogen bonds       : bond        0.04127 (  290)
  hydrogen bonds       : angle       3.64902 (  858)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2410.27 seconds
wall clock time: 41 minutes 22.66 seconds (2482.66 seconds total)