Starting phenix.real_space_refine
on Wed Sep 17 04:24:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b1l_44083/09_2025/9b1l_44083.map"
  }
  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=   0.001 sd=   0.027
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2628      2.51       5
     N     683      2.21       5
     O     700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4041
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4029
          Classifications: {'peptide': 529}
          Link IDs: {'PTRANS': 31, 'TRANS': 497}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'URC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.18, per 1000 atoms: 0.29
  Number of scatterers: 4041
  At special positions: 0
  Unit cell: (59.708, 90.86, 101.893, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     700      8.00
     N     683      7.00
     C    2628      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " distance=2.03

  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: 0.37
  Conformation dependent library (CDL) restraints added in 194.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  978

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      82.8% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 3.601A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 37
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.520A  pdb=" N   SER A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.955A  pdb=" N   ASP A  97 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.766A  pdb=" N   TRP A 105 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.895A  pdb=" N   GLN A 146 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 4.155A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 220
      removed outlier: 3.611A  pdb=" N   ALA A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLY A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 252
      removed outlier: 4.336A  pdb=" N   PHE A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   SER A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 264 through 274
      removed outlier: 4.061A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   TRP A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 304
      removed outlier: 4.198A  pdb=" N   GLN A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 311
      removed outlier: 3.594A  pdb=" N   ALA A 308 " --> pdb=" O   HIS A 305 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 325
      removed outlier: 6.245A  pdb=" N   GLU A 322 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLU A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 4.528A  pdb=" N   PHE A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   PHE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   GLY A 362 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 365 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 371
      removed outlier: 4.104A  pdb=" N   GLY A 371 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 368 through 371'
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 3.895A  pdb=" N   ILE A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 399
      removed outlier: 3.906A  pdb=" N   ALA A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 419
      removed outlier: 3.817A  pdb=" N   THR A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 425
      No H-bonds generated for 'chain 'A' and resid 423 through 425'
    Processing helix  chain 'A' and resid 426 through 455
      removed outlier: 3.672A  pdb=" N   SER A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 460 through 483
      Proline residue:  A 480  - end of helix
      removed outlier: 3.610A  pdb=" N   ARG A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 3.648A  pdb=" N   VAL A 487 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 4.506A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 500 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      Proline residue:  A 501  - end of helix
      removed outlier: 3.758A  pdb=" N   LEU A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 531
      removed outlier: 3.521A  pdb=" N   VAL A 526 " --> pdb=" O   THR A 522 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 530 " --> pdb=" O   VAL A 526 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88

    271 hydrogen bonds defined for protein.
    780 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: 0.67

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1278
        1.34 -     1.46: 964
        1.46 -     1.58: 1854
        1.58 -     1.70: 0
        1.70 -     1.82: 47
  Bond restraints: 4143
  Sorted by residual:
  bond pdb=" C2  URC A 901 "
       pdb=" O11 URC A 901 "
    ideal  model  delta    sigma   weight residual
    1.213  1.365 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" C8  URC A 901 "
       pdb=" O24 URC A 901 "
    ideal  model  delta    sigma   weight residual
    1.215  1.352 -0.137 2.00e-02 2.50e+03 4.67e+01
  bond pdb=" C6  URC A 901 "
       pdb=" O13 URC A 901 "
    ideal  model  delta    sigma   weight residual
    1.218  1.354 -0.136 2.00e-02 2.50e+03 4.65e+01
  bond pdb=" C4  URC A 901 "
       pdb=" C5  URC A 901 "
    ideal  model  delta    sigma   weight residual
    1.358  1.487 -0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C8  URC A 901 "
       pdb=" N7  URC A 901 "
    ideal  model  delta    sigma   weight residual
    1.360  1.430 -0.070 2.00e-02 2.50e+03 1.21e+01
  ... (remaining 4138 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 5583
        2.66 -     5.32: 61
        5.32 -     7.99: 5
        7.99 -    10.65: 4
       10.65 -    13.31: 3
  Bond angle restraints: 5656
  Sorted by residual:
  angle pdb=" N1  URC A 901 "
        pdb=" C2  URC A 901 "
        pdb=" N3  URC A 901 "
      ideal   model   delta    sigma   weight residual
     114.62  127.93  -13.31 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C2  URC A 901 "
        pdb=" N1  URC A 901 "
        pdb=" C6  URC A 901 "
      ideal   model   delta    sigma   weight residual
     129.31  117.43   11.88 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" N7  URC A 901 "
        pdb=" C8  URC A 901 "
        pdb=" N9  URC A 901 "
      ideal   model   delta    sigma   weight residual
     104.73  116.29  -11.56 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" C5  URC A 901 "
        pdb=" C6  URC A 901 "
        pdb=" N1  URC A 901 "
      ideal   model   delta    sigma   weight residual
     111.19  121.50  -10.31 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" N7  URC A 901 "
        pdb=" C8  URC A 901 "
        pdb=" O24 URC A 901 "
      ideal   model   delta    sigma   weight residual
     129.09  119.59    9.50 3.00e+00 1.11e-01 1.00e+01
  ... (remaining 5651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 2292
       17.32 -    34.65: 123
       34.65 -    51.97: 19
       51.97 -    69.29: 4
       69.29 -    86.62: 2
  Dihedral angle restraints: 2440
    sinusoidal: 926
      harmonic: 1514
  Sorted by residual:
  dihedral pdb=" CG  ARG A 401 "
           pdb=" CD  ARG A 401 "
           pdb=" NE  ARG A 401 "
           pdb=" CZ  ARG A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.90  -42.10     2      1.50e+01 4.44e-03 9.59e+00
  dihedral pdb=" CB  GLU A 278 "
           pdb=" CG  GLU A 278 "
           pdb=" CD  GLU A 278 "
           pdb=" OE1 GLU A 278 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.65   83.65     1      3.00e+01 1.11e-03 9.49e+00
  dihedral pdb=" CA  ASP A 335 "
           pdb=" C   ASP A 335 "
           pdb=" N   LEU A 336 "
           pdb=" CA  LEU A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.35   14.65     0      5.00e+00 4.00e-02 8.59e+00
  ... (remaining 2437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 362
       0.026 -    0.052: 204
       0.052 -    0.078: 63
       0.078 -    0.104: 27
       0.104 -    0.130: 9
  Chirality restraints: 665
  Sorted by residual:
  chirality pdb=" CA  PRO A  52 "
            pdb=" N   PRO A  52 "
            pdb=" C   PRO A  52 "
            pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  TYR A 272 "
            pdb=" N   TYR A 272 "
            pdb=" C   TYR A 272 "
            pdb=" CB  TYR A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  PRO A 501 "
            pdb=" N   PRO A 501 "
            pdb=" C   PRO A 501 "
            pdb=" CB  PRO A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.65e-01
  ... (remaining 662 not shown)

  Planarity restraints: 706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 479 "    0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 480 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 480 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 480 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 297 "    0.006 2.00e-02 2.50e+03   1.21e-02 1.47e+00
        pdb=" C   ARG A 297 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   ARG A 297 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LYS A 298 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 272 "    0.010 2.00e-02 2.50e+03   8.56e-03 1.46e+00
        pdb=" CG  TYR A 272 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 272 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 272 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 272 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 272 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 272 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 272 "    0.002 2.00e-02 2.50e+03
  ... (remaining 703 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1427
        2.86 -     3.37: 4071
        3.37 -     3.88: 6706
        3.88 -     4.39: 7810
        4.39 -     4.90: 12957
  Nonbonded interactions: 32971
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 239 "
            pdb=" OD2 ASP A 385 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" OG  SER A 279 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" O   TRP A  30 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.408 3.040
  nonbonded pdb=" OH  TYR A 451 "
            pdb=" O   PRO A 512 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" OD2 ASP A 385 "
            pdb=" NZ  LYS A 389 "
     model   vdw
     2.489 3.120
  ... (remaining 32966 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.260
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.940
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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      :  0.006   0.152   4145  Z= 0.308
  Angle     :  0.790  13.310   5660  Z= 0.389
  Chirality :  0.038   0.130    665
  Planarity :  0.005   0.032    706
  Dihedral  : 11.089  86.615   1456
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 0.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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:  0.53 (0.37), residues: 527
  helix:  0.17 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop :  1.27 (0.53), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 343 
 TYR   0.021   0.002   TYR A 272 
 PHE   0.013   0.002   PHE A 358 
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 4143)
  covalent geometry    : angle       0.78753 ( 5656)
  SS BOND              : bond        0.00137 (    2)
  SS BOND              : angle       2.28844 (    4)
  hydrogen bonds       : bond        0.11992 (  271)
  hydrogen bonds       : angle       5.46583 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7323 (ttt90)
REVERT: A  332 SER cc_start: 0.7736 (t) cc_final: 0.7193 (p)
REVERT: A  335 ASP cc_start: 0.5566 (m-30) cc_final: 0.5218 (m-30)
REVERT: A  340 PRO cc_start: 0.8075 (Cg_exo) cc_final: 0.7812 (Cg_endo)
REVERT: A  349 SER cc_start: 0.7614 (t) cc_final: 0.7403 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0738
  time to fit residues: 7.4952
Evaluate side-chains
  52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.179573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141432 restraints weight = 4495.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.01
r_work: 0.3523 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4145  Z= 0.150
  Angle     :  0.553   5.554   5660  Z= 0.281
  Chirality :  0.040   0.126    665
  Planarity :  0.005   0.035    706
  Dihedral  :  4.178  14.275    562
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.62 %
    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 aren not related in a simple way.
  whole:  1.24 (0.37), residues: 527
  helix:  0.80 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop :  1.32 (0.52), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 461 
 TYR   0.022   0.002   TYR A 272 
 PHE   0.012   0.002   PHE A 358 
 TRP   0.010   0.001   TRP A  50 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4143)
  covalent geometry    : angle       0.55154 ( 5656)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       1.67177 (    4)
  hydrogen bonds       : bond        0.05259 (  271)
  hydrogen bonds       : angle       4.29395 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   39 ASN cc_start: 0.8749 (m-40) cc_final: 0.8506 (m-40)
REVERT: A  146 GLN cc_start: 0.7662 (mt0) cc_final: 0.6979 (tp-100)
REVERT: A  166 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7736 (mmm160)
REVERT: A  332 SER cc_start: 0.7880 (t) cc_final: 0.7178 (p)
REVERT: A  335 ASP cc_start: 0.5662 (m-30) cc_final: 0.5325 (m-30)
REVERT: A  377 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7660 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0691
  time to fit residues: 5.4263
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 1 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.180329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.142136 restraints weight = 4405.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.01
r_work: 0.3534 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4145  Z= 0.131
  Angle     :  0.499   5.413   5660  Z= 0.253
  Chirality :  0.038   0.119    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.908  12.527    562
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  8.86 %
    Favored  : 88.58 %
  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:  1.57 (0.37), residues: 527
  helix:  1.19 (0.27), residues: 380
  sheet: -1.63 (1.49), residues: 10
  loop :  1.18 (0.56), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.011   0.001   PHE A  16 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4143)
  covalent geometry    : angle       0.49745 ( 5656)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       1.53081 (    4)
  hydrogen bonds       : bond        0.04832 (  271)
  hydrogen bonds       : angle       4.08362 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 SER cc_start: 0.7893 (t) cc_final: 0.7265 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0662
  time to fit residues: 5.0661
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 378 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.173019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134544 restraints weight = 4439.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.07
r_work: 0.3413 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4145  Z= 0.131
  Angle     :  0.493   5.219   5660  Z= 0.248
  Chirality :  0.037   0.115    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.803  12.113    562
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  9.79 %
    Favored  : 87.18 %
  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:  1.74 (0.38), residues: 527
  helix:  1.32 (0.27), residues: 380
  sheet: -1.86 (1.60), residues: 10
  loop :  1.29 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 121 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.010   0.001   PHE A 358 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4143)
  covalent geometry    : angle       0.49159 ( 5656)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       1.39179 (    4)
  hydrogen bonds       : bond        0.04681 (  271)
  hydrogen bonds       : angle       4.02597 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0564
  time to fit residues: 4.0611
Evaluate side-chains
  51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   chunk 51 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.174023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136135 restraints weight = 4425.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.01
r_work: 0.3432 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4145  Z= 0.115
  Angle     :  0.469   5.385   5660  Z= 0.235
  Chirality :  0.037   0.119    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.649  11.715    562
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  :  9.79 %
    Favored  : 87.41 %
  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:  1.95 (0.38), residues: 527
  helix:  1.48 (0.27), residues: 381
  sheet: -1.69 (1.77), residues: 10
  loop :  1.33 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 253 
 TYR   0.018   0.002   TYR A 272 
 PHE   0.010   0.001   PHE A 266 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4143)
  covalent geometry    : angle       0.46802 ( 5656)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       1.25789 (    4)
  hydrogen bonds       : bond        0.04343 (  271)
  hydrogen bonds       : angle       3.93805 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 8
  residues processed: 54
  average time/residue: 0.0566
  time to fit residues: 4.1022
Evaluate side-chains
  51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.173030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.134984 restraints weight = 4506.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.03
r_work: 0.3422 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4145  Z= 0.123
  Angle     :  0.480   5.435   5660  Z= 0.238
  Chirality :  0.037   0.119    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.634  11.616    562
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.19 %
    Favored  : 86.71 %
  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:  1.93 (0.38), residues: 527
  helix:  1.49 (0.27), residues: 380
  sheet: -1.72 (1.85), residues: 10
  loop :  1.25 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 169 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.010   0.001   PHE A 266 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4143)
  covalent geometry    : angle       0.47916 ( 5656)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       1.24516 (    4)
  hydrogen bonds       : bond        0.04446 (  271)
  hydrogen bonds       : angle       3.93406 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0578
  time to fit residues: 3.9114
Evaluate side-chains
  51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  451 TYR
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.173023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.134263 restraints weight = 4520.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.10
r_work: 0.3406 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4145  Z= 0.132
  Angle     :  0.487   5.474   5660  Z= 0.242
  Chirality :  0.037   0.118    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.651  11.856    562
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.19 %
    Favored  : 86.48 %
  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:  1.89 (0.38), residues: 527
  helix:  1.43 (0.27), residues: 381
  sheet: -1.92 (1.74), residues: 10
  loop :  1.32 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 169 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.011   0.001   PHE A 358 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4143)
  covalent geometry    : angle       0.48601 ( 5656)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       1.24476 (    4)
  hydrogen bonds       : bond        0.04589 (  271)
  hydrogen bonds       : angle       3.96601 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0558
  time to fit residues: 3.7719
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0050
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.173609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135618 restraints weight = 4433.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.02
r_work: 0.3432 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4145  Z= 0.116
  Angle     :  0.468   5.495   5660  Z= 0.232
  Chirality :  0.037   0.119    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.545  11.651    562
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.89 %
    Favored  : 86.48 %
  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:  2.03 (0.38), residues: 527
  helix:  1.55 (0.27), residues: 381
  sheet: -2.00 (1.74), residues: 10
  loop :  1.37 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 461 
 TYR   0.018   0.002   TYR A 272 
 PHE   0.010   0.001   PHE A 201 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4143)
  covalent geometry    : angle       0.46693 ( 5656)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       1.15814 (    4)
  hydrogen bonds       : bond        0.04255 (  271)
  hydrogen bonds       : angle       3.87753 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  438 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7024 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 48
  average time/residue: 0.0621
  time to fit residues: 4.1495
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0570
   chunk 46 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.173249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134841 restraints weight = 4540.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.10
r_work: 0.3416 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4145  Z= 0.121
  Angle     :  0.475   5.499   5660  Z= 0.235
  Chirality :  0.037   0.120    665
  Planarity :  0.004   0.035    706
  Dihedral  :  3.542  11.816    562
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.19 %
    Favored  : 86.71 %
  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:  2.06 (0.38), residues: 527
  helix:  1.57 (0.27), residues: 381
  sheet: -1.97 (1.75), residues: 10
  loop :  1.36 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 121 
 TYR   0.019   0.002   TYR A 272 
 PHE   0.010   0.001   PHE A 266 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4143)
  covalent geometry    : angle       0.47444 ( 5656)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       1.15810 (    4)
  hydrogen bonds       : bond        0.04361 (  271)
  hydrogen bonds       : angle       3.88962 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 ASP cc_start: 0.8020 (t70) cc_final: 0.7429 (t0)
REVERT: A  438 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7202 (tt)
  outliers start: 9
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0609
  time to fit residues: 3.9725
Evaluate side-chains
  50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  307 GLU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 39 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 49 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.175343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137541 restraints weight = 4416.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.01
r_work: 0.3454 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4145  Z= 0.104
  Angle     :  0.454   5.491   5660  Z= 0.224
  Chirality :  0.036   0.120    665
  Planarity :  0.004   0.036    706
  Dihedral  :  3.413  11.343    562
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.66 %
    Favored  : 86.71 %
  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:  2.24 (0.38), residues: 527
  helix:  1.72 (0.27), residues: 381
  sheet: -1.92 (1.74), residues: 10
  loop :  1.36 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 253 
 TYR   0.017   0.001   TYR A 272 
 PHE   0.010   0.001   PHE A 201 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 4143)
  covalent geometry    : angle       0.45359 ( 5656)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       1.08438 (    4)
  hydrogen bonds       : bond        0.03948 (  271)
  hydrogen bonds       : angle       3.77982 (  780)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 ASP cc_start: 0.7950 (t70) cc_final: 0.7328 (t0)
REVERT: A  438 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.7006 (tt)
  outliers start: 7
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0570
  time to fit residues: 3.9645
Evaluate side-chains
  49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  482 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.172568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134165 restraints weight = 4479.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.08
r_work: 0.3408 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4145  Z= 0.136
  Angle     :  0.494   5.506   5660  Z= 0.243
  Chirality :  0.038   0.119    665
  Planarity :  0.004   0.036    706
  Dihedral  :  3.568  12.164    562
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.89 %
    Favored  : 86.48 %
  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:  2.04 (0.38), residues: 527
  helix:  1.57 (0.27), residues: 381
  sheet: -1.94 (1.76), residues: 10
  loop :  1.33 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 483 
 TYR   0.020   0.002   TYR A 272 
 PHE   0.012   0.001   PHE A 361 
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4143)
  covalent geometry    : angle       0.49308 ( 5656)
  SS BOND              : bond        0.00177 (    2)
  SS BOND              : angle       1.16435 (    4)
  hydrogen bonds       : bond        0.04575 (  271)
  hydrogen bonds       : angle       3.93693 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1369.19 seconds
wall clock time: 24 minutes 5.89 seconds (1445.89 seconds total)