Starting phenix.real_space_refine
on Sat May  2 09:38:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkj_61563/05_2026/9jkj_61563.map"
  }
  resolution = 2.69
  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=  -0.003 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     Cl      1      4.86       5
     Na      2      4.78       5
     C    2802      2.51       5
     N     660      2.21       5
     O     715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4203
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4185
          Classifications: {'peptide': 530}
          Link IDs: {'PTRANS': 23, 'TRANS': 506}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 18
          Unusual residues: {' CL': 1, ' NA': 2, 'LDP': 1}
          Classifications: {'undetermined': 4, 'water': 4}
          Link IDs: {None: 7}
  Time building chain proxies: 1.04, per 1000 atoms: 0.25
  Number of scatterers: 4203
  At special positions: 0
  Unit cell: (75.0537, 65.7774, 84.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      23     16.00
     Na      2     11.00
     O     715      8.00
     N     660      7.00
     C    2802      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 189 " 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: 0.30
  Conformation dependent library (CDL) restraints added in 169.8 milliseconds
  

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 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:
      36 helices and 1 sheets defined
      80.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 78
      removed outlier: 3.734A  pdb=" N   SER A  72 " --> pdb=" O   ASP A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.559A  pdb=" N   VAL A  83 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 93
      removed outlier: 3.895A  pdb=" N   TYR A  88 " --> pdb=" O   TRP A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 109
      removed outlier: 3.671A  pdb=" N   LEU A  99 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
      Proline residue:  A 101  - end of helix
    Processing helix  chain 'A' and resid 110 through 125
    Processing helix  chain 'A' and resid 135 through 138
    Processing helix  chain 'A' and resid 139 through 169
      removed outlier: 3.602A  pdb=" N   PHE A 143 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 159 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 219
      removed outlier: 3.559A  pdb=" N   GLU A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 237 through 253
      removed outlier: 3.828A  pdb=" N   CYS A 243 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 247 " --> pdb=" O   CYS A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 286
      removed outlier: 3.508A  pdb=" N   VAL A 275 " --> pdb=" O   THR A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 298
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 308 through 323
    Processing helix  chain 'A' and resid 327 through 334
    Processing helix  chain 'A' and resid 343 through 350
    Processing helix  chain 'A' and resid 350 through 376
      removed outlier: 3.591A  pdb=" N   GLN A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 382
      removed outlier: 3.610A  pdb=" N   VAL A 382 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.540A  pdb=" N   TYR A 394 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      Proline residue:  A 395  - end of helix
      removed outlier: 4.179A  pdb=" N   THR A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 419
      removed outlier: 3.749A  pdb=" N   VAL A 410 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 439
      removed outlier: 3.810A  pdb=" N   VAL A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 434 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 436 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU A 437 " --> pdb=" O   GLY A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 443
      removed outlier: 3.798A  pdb=" N   ARG A 443 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 440 through 443'
    Processing helix  chain 'A' and resid 444 through 460
      removed outlier: 3.907A  pdb=" N   PHE A 451 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.634A  pdb=" N   THR A 465 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 479
      removed outlier: 3.710A  pdb=" N   VAL A 471 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 497
    Processing helix  chain 'A' and resid 500 through 513
    Processing helix  chain 'A' and resid 517 through 526
    Processing helix  chain 'A' and resid 526 through 542
      removed outlier: 3.538A  pdb=" N   VAL A 535 " --> pdb=" O   PHE A 531 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE A 540 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 570
      removed outlier: 3.629A  pdb=" N   ILE A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   MET A 569 " --> pdb=" O   ALA A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 582
      removed outlier: 3.538A  pdb=" N   ALA A 577 " --> pdb=" O   PRO A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 596
      removed outlier: 3.638A  pdb=" N   LEU A 591 " --> pdb=" O   PHE A 587 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 592 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A 594 " --> pdb=" O   LYS A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 599
      No H-bonds generated for 'chain 'A' and resid 597 through 599'
    Processing helix  chain 'A' and resid 600 through 607
    Processing helix  chain 'A' and resid 609 through 612
    Processing helix  chain 'A' and resid 613 through 618
      removed outlier: 4.297A  pdb=" N   TRP A 617 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 613 through 618'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548

    246 hydrogen bonds defined for protein.
    711 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: 0.54

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 625
        1.30 -     1.43: 1272
        1.43 -     1.56: 2395
        1.56 -     1.68: 0
        1.68 -     1.81: 34
  Bond restraints: 4326
  Sorted by residual:
  bond pdb=" C   ASN A 353 "
       pdb=" O   ASN A 353 "
    ideal  model  delta    sigma   weight residual
    1.237  1.173  0.063 1.31e-02 5.83e+03 2.33e+01
  bond pdb=" C   ILE A 352 "
       pdb=" N   ASN A 353 "
    ideal  model  delta    sigma   weight residual
    1.333  1.297  0.035 1.50e-02 4.44e+03 5.50e+00
  bond pdb=" C3  LDP A 701 "
       pdb=" O1  LDP A 701 "
    ideal  model  delta    sigma   weight residual
    1.353  1.399 -0.046 2.00e-02 2.50e+03 5.19e+00
  bond pdb=" C4  LDP A 701 "
       pdb=" O2  LDP A 701 "
    ideal  model  delta    sigma   weight residual
    1.355  1.398 -0.043 2.00e-02 2.50e+03 4.67e+00
  bond pdb=" C   ASN A 353 "
       pdb=" N   SER A 354 "
    ideal  model  delta    sigma   weight residual
    1.334  1.309  0.025 1.46e-02 4.69e+03 2.95e+00
  ... (remaining 4321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 5780
        1.64 -     3.28: 101
        3.28 -     4.92: 22
        4.92 -     6.56: 0
        6.56 -     8.21: 2
  Bond angle restraints: 5905
  Sorted by residual:
  angle pdb=" C   PHE A 438 "
        pdb=" N   GLN A 439 "
        pdb=" CA  GLN A 439 "
      ideal   model   delta    sigma   weight residual
     121.54  128.54   -7.00 1.91e+00 2.74e-01 1.34e+01
  angle pdb=" N   GLY A  95 "
        pdb=" CA  GLY A  95 "
        pdb=" C   GLY A  95 "
      ideal   model   delta    sigma   weight residual
     111.67  114.91   -3.24 9.20e-01 1.18e+00 1.24e+01
  angle pdb=" N   ASN A 353 "
        pdb=" CA  ASN A 353 "
        pdb=" C   ASN A 353 "
      ideal   model   delta    sigma   weight residual
     112.90  108.92    3.98 1.31e+00 5.83e-01 9.22e+00
  angle pdb=" O   ILE A 352 "
        pdb=" C   ILE A 352 "
        pdb=" N   ASN A 353 "
      ideal   model   delta    sigma   weight residual
     122.05  118.45    3.60 1.31e+00 5.83e-01 7.56e+00
  angle pdb=" CA  ILE A 352 "
        pdb=" C   ILE A 352 "
        pdb=" N   ASN A 353 "
      ideal   model   delta    sigma   weight residual
     118.05  121.57   -3.52 1.40e+00 5.10e-01 6.32e+00
  ... (remaining 5900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.81: 2348
       14.81 -    29.62: 74
       29.62 -    44.43: 13
       44.43 -    59.25: 1
       59.25 -    74.06: 1
  Dihedral angle restraints: 2437
    sinusoidal: 910
      harmonic: 1527
  Sorted by residual:
  dihedral pdb=" CA  TRP A 132 "
           pdb=" C   TRP A 132 "
           pdb=" N   LYS A 133 "
           pdb=" CA  LYS A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.09   20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  PHE A 412 "
           pdb=" C   PHE A 412 "
           pdb=" N   ILE A 413 "
           pdb=" CA  ILE A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.68   16.32     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ASN A 336 "
           pdb=" C   ASN A 336 "
           pdb=" N   LYS A 337 "
           pdb=" CA  LYS A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  ... (remaining 2434 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 391
       0.031 -    0.061: 212
       0.061 -    0.091: 45
       0.091 -    0.122: 18
       0.122 -    0.152: 3
  Chirality restraints: 669
  Sorted by residual:
  chirality pdb=" CA  GLN A 439 "
            pdb=" N   GLN A 439 "
            pdb=" C   GLN A 439 "
            pdb=" CB  GLN A 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CG  LEU A 403 "
            pdb=" CB  LEU A 403 "
            pdb=" CD1 LEU A 403 "
            pdb=" CD2 LEU A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  PRO A 236 "
            pdb=" N   PRO A 236 "
            pdb=" C   PRO A 236 "
            pdb=" CB  PRO A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 666 not shown)

  Planarity restraints: 722
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 256 "    0.014 2.00e-02 2.50e+03   1.37e-02 4.70e+00
        pdb=" CG  TRP A 256 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 256 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 256 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 256 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 256 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 256 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 256 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 256 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 256 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 235 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.04e+00
        pdb=" N   PRO A 236 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 236 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 236 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 111 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.80e+00
        pdb=" N   PRO A 112 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 719 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 13
        2.29 -     2.94: 1822
        2.94 -     3.59: 6129
        3.59 -     4.25: 10849
        4.25 -     4.90: 17458
  Nonbonded interactions: 36271
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  75 "
            pdb="NA    NA A 702 "
     model   vdw
     1.634 2.470
  nonbonded pdb=" O   SER A 321 "
            pdb="NA    NA A 703 "
     model   vdw
     1.800 2.470
  nonbonded pdb=" O   ALA A  77 "
            pdb="NA    NA A 703 "
     model   vdw
     1.981 2.470
  nonbonded pdb=" OH  TYR A 593 "
            pdb=" OD1 ASP A 605 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" O   ASP A 232 "
     model   vdw
     2.096 3.040
  ... (remaining 36266 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:             0.980
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.310
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
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      :  0.003   0.063   4327  Z= 0.173
  Angle     :  0.572   8.206   5907  Z= 0.329
  Chirality :  0.038   0.152    669
  Planarity :  0.005   0.050    722
  Dihedral  :  8.472  74.058   1458
  Min Nonbonded Distance : 1.634

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.16 (0.29), residues: 524
  helix: -4.10 (0.16), residues: 347
  sheet:  None (None), residues: 0
  loop : -1.35 (0.47), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.018   0.002   TYR A 115 
 PHE   0.012   0.001   PHE A 365 
 TRP   0.037   0.002   TRP A 256 
 HIS   0.003   0.001   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4326)
  covalent geometry    : angle       0.57199 ( 5905)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       1.18108 (    2)
  hydrogen bonds       : bond        0.29892 (  246)
  hydrogen bonds       : angle      11.28254 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  531 PHE cc_start: 0.6817 (m-10) cc_final: 0.6589 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.5108
  time to fit residues: 63.4231
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   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 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.136262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.112998 restraints weight = 4861.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.67
r_work: 0.3147 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4327  Z= 0.137
  Angle     :  0.636   9.934   5907  Z= 0.321
  Chirality :  0.041   0.141    669
  Planarity :  0.005   0.051    722
  Dihedral  :  4.745  26.322    571
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.69 %
    Favored  : 86.29 %
  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: -2.44 (0.33), residues: 524
  helix: -1.77 (0.22), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.70 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 295 
 TYR   0.027   0.002   TYR A 115 
 PHE   0.013   0.001   PHE A  76 
 TRP   0.013   0.001   TRP A 132 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4326)
  covalent geometry    : angle       0.63643 ( 5905)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.32372 (    2)
  hydrogen bonds       : bond        0.04494 (  246)
  hydrogen bonds       : angle       5.16619 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8638 (tt) cc_final: 0.8321 (tm)
REVERT: A  272 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7532 (tpp)
REVERT: A  531 PHE cc_start: 0.7159 (m-10) cc_final: 0.6824 (m-80)
REVERT: A  534 PHE cc_start: 0.7896 (t80) cc_final: 0.7552 (t80)
REVERT: A  608 GLU cc_start: 0.6691 (mp0) cc_final: 0.6186 (pm20)
  outliers start: 9
  outliers final: 1
  residues processed: 72
  average time/residue: 0.3960
  time to fit residues: 29.8614
Evaluate side-chains
  56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  272 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.110857 restraints weight = 4880.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.64
r_work: 0.3090 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4327  Z= 0.136
  Angle     :  0.590   9.128   5907  Z= 0.296
  Chirality :  0.040   0.142    669
  Planarity :  0.004   0.049    722
  Dihedral  :  4.577  27.246    571
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.83 %
    Favored  : 83.15 %
  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: -0.57 (0.35), residues: 524
  helix: -0.14 (0.26), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.59 (0.49), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 295 
 TYR   0.023   0.002   TYR A 115 
 PHE   0.012   0.001   PHE A  76 
 TRP   0.012   0.001   TRP A 132 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4326)
  covalent geometry    : angle       0.59025 ( 5905)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.21228 (    2)
  hydrogen bonds       : bond        0.04084 (  246)
  hydrogen bonds       : angle       4.60936 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  531 PHE cc_start: 0.7288 (m-10) cc_final: 0.6951 (m-80)
REVERT: A  534 PHE cc_start: 0.7910 (t80) cc_final: 0.7534 (t80)
REVERT: A  608 GLU cc_start: 0.6672 (mp0) cc_final: 0.6259 (pm20)
  outliers start: 9
  outliers final: 4
  residues processed: 70
  average time/residue: 0.4524
  time to fit residues: 33.0402
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.136692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113280 restraints weight = 4856.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.64
r_work: 0.3154 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4327  Z= 0.108
  Angle     :  0.546   8.852   5907  Z= 0.271
  Chirality :  0.039   0.141    669
  Planarity :  0.004   0.046    722
  Dihedral  :  4.349  27.660    571
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.51 %
    Favored  : 82.25 %
  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:  0.37 (0.36), residues: 524
  helix:  0.64 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.48 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.019   0.001   TYR A 115 
 PHE   0.011   0.001   PHE A  76 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4326)
  covalent geometry    : angle       0.54658 ( 5905)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.12405 (    2)
  hydrogen bonds       : bond        0.03539 (  246)
  hydrogen bonds       : angle       4.31149 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  531 PHE cc_start: 0.7218 (m-10) cc_final: 0.6822 (m-80)
REVERT: A  534 PHE cc_start: 0.7886 (t80) cc_final: 0.7535 (t80)
REVERT: A  608 GLU cc_start: 0.6734 (mp0) cc_final: 0.6291 (pm20)
  outliers start: 10
  outliers final: 4
  residues processed: 65
  average time/residue: 0.4584
  time to fit residues: 31.1023
Evaluate side-chains
  59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.134690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111315 restraints weight = 4865.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.63
r_work: 0.3136 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4327  Z= 0.131
  Angle     :  0.561   8.521   5907  Z= 0.279
  Chirality :  0.040   0.140    669
  Planarity :  0.004   0.047    722
  Dihedral  :  4.396  28.639    571
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.06 %
    Favored  : 82.25 %
  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:  0.68 (0.37), residues: 524
  helix:  0.90 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.47 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 295 
 TYR   0.021   0.002   TYR A 115 
 PHE   0.012   0.001   PHE A  76 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.005   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4326)
  covalent geometry    : angle       0.56071 ( 5905)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.19264 (    2)
  hydrogen bonds       : bond        0.03778 (  246)
  hydrogen bonds       : angle       4.30360 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  531 PHE cc_start: 0.7325 (m-10) cc_final: 0.6930 (m-80)
REVERT: A  534 PHE cc_start: 0.7917 (t80) cc_final: 0.7545 (t80)
REVERT: A  608 GLU cc_start: 0.6802 (mp0) cc_final: 0.6315 (pm20)
  outliers start: 12
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4105
  time to fit residues: 31.5036
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0970
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 373 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110635 restraints weight = 4956.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.70
r_work: 0.3123 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4327  Z= 0.111
  Angle     :  0.537   8.376   5907  Z= 0.267
  Chirality :  0.039   0.128    669
  Planarity :  0.004   0.047    722
  Dihedral  :  4.278  28.662    571
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.38 %
    Favored  : 82.02 %
  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:  0.97 (0.37), residues: 524
  helix:  1.14 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.41 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 295 
 TYR   0.019   0.002   TYR A  88 
 PHE   0.014   0.001   PHE A  76 
 TRP   0.010   0.001   TRP A 132 
 HIS   0.003   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4326)
  covalent geometry    : angle       0.53694 ( 5905)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.11059 (    2)
  hydrogen bonds       : bond        0.03508 (  246)
  hydrogen bonds       : angle       4.18520 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7894 (mt0)
REVERT: A  531 PHE cc_start: 0.7293 (m-10) cc_final: 0.6936 (m-80)
REVERT: A  534 PHE cc_start: 0.7869 (t80) cc_final: 0.7500 (t80)
REVERT: A  608 GLU cc_start: 0.6812 (mp0) cc_final: 0.6332 (pm20)
  outliers start: 16
  outliers final: 6
  residues processed: 76
  average time/residue: 0.4115
  time to fit residues: 32.7237
Evaluate side-chains
  66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0170
   chunk 24 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.133261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109105 restraints weight = 5027.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.70
r_work: 0.3115 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4327  Z= 0.113
  Angle     :  0.534   8.312   5907  Z= 0.266
  Chirality :  0.039   0.129    669
  Planarity :  0.004   0.046    722
  Dihedral  :  4.245  28.773    571
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.51 %
    Favored  : 81.57 %
  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:  1.11 (0.37), residues: 524
  helix:  1.25 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.39 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 295 
 TYR   0.017   0.001   TYR A 115 
 PHE   0.013   0.001   PHE A  76 
 TRP   0.009   0.001   TRP A 132 
 HIS   0.003   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4326)
  covalent geometry    : angle       0.53419 ( 5905)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       0.13765 (    2)
  hydrogen bonds       : bond        0.03504 (  246)
  hydrogen bonds       : angle       4.17580 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7844 (mt0)
REVERT: A  531 PHE cc_start: 0.7236 (m-10) cc_final: 0.6862 (m-80)
REVERT: A  534 PHE cc_start: 0.7870 (t80) cc_final: 0.7497 (t80)
REVERT: A  608 GLU cc_start: 0.6782 (mp0) cc_final: 0.6389 (pm20)
  outliers start: 13
  outliers final: 6
  residues processed: 73
  average time/residue: 0.4108
  time to fit residues: 31.4145
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109228 restraints weight = 4880.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.68
r_work: 0.3083 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4327  Z= 0.138
  Angle     :  0.565   9.161   5907  Z= 0.282
  Chirality :  0.040   0.141    669
  Planarity :  0.004   0.048    722
  Dihedral  :  4.322  28.943    571
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.96 %
    Favored  : 81.12 %
  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:  1.08 (0.37), residues: 524
  helix:  1.21 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.33 (0.51), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.020   0.002   TYR A 115 
 PHE   0.013   0.001   PHE A 531 
 TRP   0.012   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4326)
  covalent geometry    : angle       0.56555 ( 5905)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.19364 (    2)
  hydrogen bonds       : bond        0.03766 (  246)
  hydrogen bonds       : angle       4.28854 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7851 (mt0)
REVERT: A  531 PHE cc_start: 0.7097 (m-10) cc_final: 0.6667 (m-80)
REVERT: A  534 PHE cc_start: 0.7891 (t80) cc_final: 0.7501 (t80)
REVERT: A  608 GLU cc_start: 0.6761 (mp0) cc_final: 0.6401 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 72
  average time/residue: 0.3962
  time to fit residues: 29.9180
Evaluate side-chains
  68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.132992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109156 restraints weight = 4962.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.67
r_work: 0.3084 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4327  Z= 0.135
  Angle     :  0.566  10.338   5907  Z= 0.281
  Chirality :  0.040   0.141    669
  Planarity :  0.004   0.048    722
  Dihedral  :  4.320  29.113    571
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.18 %
    Favored  : 81.35 %
  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:  1.11 (0.37), residues: 524
  helix:  1.25 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.34 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.013   0.001   PHE A 531 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4326)
  covalent geometry    : angle       0.56625 ( 5905)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.17920 (    2)
  hydrogen bonds       : bond        0.03748 (  246)
  hydrogen bonds       : angle       4.27149 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7818 (mt0)
REVERT: A  531 PHE cc_start: 0.7215 (m-10) cc_final: 0.6794 (m-80)
REVERT: A  534 PHE cc_start: 0.7900 (t80) cc_final: 0.7541 (t80)
REVERT: A  608 GLU cc_start: 0.6814 (mp0) cc_final: 0.6457 (pm20)
  outliers start: 11
  outliers final: 7
  residues processed: 70
  average time/residue: 0.3593
  time to fit residues: 26.4310
Evaluate side-chains
  71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   overall best weight:    0.5158

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.111313 restraints weight = 4910.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.67
r_work: 0.3112 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4327  Z= 0.107
  Angle     :  0.542  11.558   5907  Z= 0.267
  Chirality :  0.039   0.125    669
  Planarity :  0.004   0.045    722
  Dihedral  :  4.165  28.804    571
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.08 %
    Favored  : 81.12 %
  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:  1.35 (0.37), residues: 524
  helix:  1.40 (0.27), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.22 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.014   0.001   TYR A 115 
 PHE   0.011   0.001   PHE A 531 
 TRP   0.008   0.001   TRP A 132 
 HIS   0.003   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4326)
  covalent geometry    : angle       0.54184 ( 5905)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.15481 (    2)
  hydrogen bonds       : bond        0.03383 (  246)
  hydrogen bonds       : angle       4.16033 (  711)

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

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

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1048 Ramachandran restraints generated.
    524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7718 (mt0)
REVERT: A  531 PHE cc_start: 0.7213 (m-10) cc_final: 0.6797 (m-80)
REVERT: A  534 PHE cc_start: 0.7895 (t80) cc_final: 0.7517 (t80)
REVERT: A  593 TYR cc_start: 0.8101 (m-80) cc_final: 0.7876 (m-10)
REVERT: A  608 GLU cc_start: 0.6850 (mp0) cc_final: 0.6532 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 71
  average time/residue: 0.3151
  time to fit residues: 23.5686
Evaluate side-chains
  69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.133418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.109367 restraints weight = 4886.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.68
r_work: 0.3076 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4327  Z= 0.141
  Angle     :  0.576  11.474   5907  Z= 0.286
  Chirality :  0.040   0.142    669
  Planarity :  0.004   0.048    722
  Dihedral  :  4.319  29.371    571
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.08 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.37), residues: 524
  helix:  1.32 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.31 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 295 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.015   0.001   PHE A 531 
 TRP   0.012   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4326)
  covalent geometry    : angle       0.57578 ( 5905)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.20911 (    2)
  hydrogen bonds       : bond        0.03796 (  246)
  hydrogen bonds       : angle       4.29242 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.07 seconds
wall clock time: 25 minutes 12.04 seconds (1512.04 seconds total)