Starting phenix.real_space_refine
on Wed Jul  1 23:47:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkj_61563/07_2026/9jkj_61563_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkj_61563/07_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_61563/07_2026/9jkj_61563_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkj_61563/07_2026/9jkj_61563_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jkj_61563/07_2026/9jkj_61563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkj_61563/07_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 15
          Ad-hoc single atom residues: {' NA': 2, ' CL': 1}
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1, 'water': 4}
          Link IDs: {None: 3}
          Chain breaks: 3
  Time building chain proxies: 1.03, 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: 0.36
  Conformation dependent library (CDL) restraints added in 158.2 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: 0.17
  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: 0.47

  Time building geometry restraints manager: 0.49 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 3.210
  nonbonded pdb=" O   SER A 321 "
            pdb="NA    NA A 703 "
     model   vdw
     1.800 3.210
  nonbonded pdb=" O   ALA A  77 "
            pdb="NA    NA A 703 "
     model   vdw
     1.981 3.210
  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:             1.060
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.260
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
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/Z
  covalent geometry    : bond        0.00329 /  0.17 ( 4326)
  covalent geometry    : angle       0.57199 /  0.33 ( 5905)
  SS BOND              : bond        0.00047 /  0.02 (    1)
  SS BOND              : angle       1.18108 /  0.64 (    2)
  hydrogen bonds       : bond        0.29892 / 18.97 (  246)
  hydrogen bonds       : angle      11.28254 /  7.58 (  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  : 0.149 
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: 0.5086
  time to fit residues: 63.2379
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  : 0.152 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 124 ASN
A 353 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.135641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.112825 restraints weight = 4868.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.64
r_work: 0.3140 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4327  Z= 0.143
  Angle     :  0.642   9.899   5907  Z= 0.324
  Chirality :  0.042   0.144    669
  Planarity :  0.005   0.052    722
  Dihedral  :  4.778  23.851    571
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.91 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.33), residues: 524
  helix: -1.77 (0.22), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.69 (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   0.002   PHE A  76 
 TRP   0.013   0.001   TRP A 132 
 HIS   0.002   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 4326)
  covalent geometry    : angle       0.64251 /  0.32 ( 5905)
  SS BOND              : bond        0.00097 /  0.05 (    1)
  SS BOND              : angle       0.32433 /  0.17 (    2)
  hydrogen bonds       : bond        0.04426 /  2.82 (  246)
  hydrogen bonds       : angle       5.14765 /  3.43 (  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
  79 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8617 (tt) cc_final: 0.8311 (tm)
REVERT: A  272 MET cc_start: 0.7793 (mmm) cc_final: 0.7535 (tpp)
REVERT: A  531 PHE cc_start: 0.7148 (m-10) cc_final: 0.6818 (m-80)
REVERT: A  534 PHE cc_start: 0.7889 (t80) cc_final: 0.7541 (t80)
REVERT: A  608 GLU cc_start: 0.6669 (mp0) cc_final: 0.6231 (pm20)
  outliers start: 10
  outliers final: 2
  residues processed: 76
  average time/residue: 0.4065
  time to fit residues: 32.4519
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  409 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0050
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.112041 restraints weight = 4908.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.68
r_work: 0.3158 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2858

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= 0.118
  Angle     :  0.569   9.186   5907  Z= 0.285
  Chirality :  0.039   0.130    669
  Planarity :  0.004   0.046    722
  Dihedral  :  4.483  26.729    571
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.93 %
    Favored  : 83.60 %
  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 are not related in a simple way.
  whole: -0.40 (0.35), residues: 524
  helix: -0.01 (0.26), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.55 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 295 
 TYR   0.020   0.002   TYR A 115 
 PHE   0.009   0.001   PHE A  76 
 TRP   0.009   0.001   TRP A 132 
 HIS   0.001   0.000   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 4326)
  covalent geometry    : angle       0.56876 /  0.29 ( 5905)
  SS BOND              : bond        0.00133 /  0.07 (    1)
  SS BOND              : angle       0.17794 /  0.09 (    2)
  hydrogen bonds       : bond        0.03816 /  2.42 (  246)
  hydrogen bonds       : angle       4.49060 /  2.99 (  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
  74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  301 ASP cc_start: 0.7254 (p0) cc_final: 0.6950 (p0)
REVERT: A  531 PHE cc_start: 0.7258 (m-10) cc_final: 0.6925 (m-80)
REVERT: A  534 PHE cc_start: 0.7892 (t80) cc_final: 0.7538 (t80)
REVERT: A  608 GLU cc_start: 0.6700 (mp0) cc_final: 0.6298 (pm20)
  outliers start: 11
  outliers final: 4
  residues processed: 72
  average time/residue: 0.4331
  time to fit residues: 32.6453
Evaluate side-chains
  60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.110183 restraints weight = 4906.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.65
r_work: 0.3131 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4327  Z= 0.127
  Angle     :  0.565   8.902   5907  Z= 0.282
  Chirality :  0.040   0.143    669
  Planarity :  0.004   0.047    722
  Dihedral  :  4.430  28.954    571
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.06 %
    Favored  : 82.47 %
  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:  0.31 (0.36), residues: 524
  helix:  0.58 (0.27), residues: 368
  sheet:  None (None), residues: 0
  loop : -0.46 (0.51), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 295 
 TYR   0.022   0.002   TYR A 115 
 PHE   0.013   0.001   PHE A  76 
 TRP   0.014   0.001   TRP A 132 
 HIS   0.005   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 4326)
  covalent geometry    : angle       0.56540 /  0.28 ( 5905)
  SS BOND              : bond        0.00047 /  0.02 (    1)
  SS BOND              : angle       0.18002 /  0.10 (    2)
  hydrogen bonds       : bond        0.03760 /  2.39 (  246)
  hydrogen bonds       : angle       4.32962 /  2.88 (  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
  70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  531 PHE cc_start: 0.7207 (m-10) cc_final: 0.6817 (m-80)
REVERT: A  534 PHE cc_start: 0.7892 (t80) cc_final: 0.7533 (t80)
REVERT: A  608 GLU cc_start: 0.6728 (mp0) cc_final: 0.6207 (pm20)
  outliers start: 11
  outliers final: 4
  residues processed: 67
  average time/residue: 0.4138
  time to fit residues: 29.0434
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  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:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 ASN
A 223 HIS
A 353 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.135872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.112534 restraints weight = 4849.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.63
r_work: 0.3123 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4327  Z= 0.121
  Angle     :  0.552   8.544   5907  Z= 0.274
  Chirality :  0.040   0.133    669
  Planarity :  0.004   0.048    722
  Dihedral  :  4.360  29.577    571
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.28 %
    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:  0.72 (0.37), residues: 524
  helix:  0.91 (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   0.002   0.000   ARG A 295 
 TYR   0.020   0.002   TYR A 115 
 PHE   0.011   0.001   PHE A  76 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 4326)
  covalent geometry    : angle       0.55225 /  0.27 ( 5905)
  SS BOND              : bond        0.00012 /  0.01 (    1)
  SS BOND              : angle       0.16406 /  0.09 (    2)
  hydrogen bonds       : bond        0.03650 /  2.31 (  246)
  hydrogen bonds       : angle       4.24434 /  2.81 (  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
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  534 PHE cc_start: 0.7917 (t80) cc_final: 0.7562 (t80)
REVERT: A  608 GLU cc_start: 0.6820 (mp0) cc_final: 0.6354 (pm20)
  outliers start: 12
  outliers final: 5
  residues processed: 73
  average time/residue: 0.3660
  time to fit residues: 28.0542
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.131541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.107479 restraints weight = 4952.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.69
r_work: 0.3038 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4327  Z= 0.203
  Angle     :  0.625   8.369   5907  Z= 0.314
  Chirality :  0.044   0.165    669
  Planarity :  0.005   0.051    722
  Dihedral  :  4.675  29.895    571
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 14.61 %
    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:  0.44 (0.36), residues: 524
  helix:  0.74 (0.27), residues: 367
  sheet:  None (None), residues: 0
  loop : -0.57 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.026   0.002   TYR A 115 
 PHE   0.014   0.002   PHE A  76 
 TRP   0.016   0.001   TRP A 132 
 HIS   0.006   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.20 ( 4326)
  covalent geometry    : angle       0.62546 /  0.31 ( 5905)
  SS BOND              : bond        0.00077 /  0.04 (    1)
  SS BOND              : angle       0.35791 /  0.21 (    2)
  hydrogen bonds       : bond        0.04373 /  2.74 (  246)
  hydrogen bonds       : angle       4.47068 /  2.99 (  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: 17
    poor density    : 63
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7946 (mt0)
REVERT: A  534 PHE cc_start: 0.7949 (t80) cc_final: 0.7587 (t80)
REVERT: A  608 GLU cc_start: 0.6751 (mp0) cc_final: 0.6256 (pm20)
  outliers start: 17
  outliers final: 7
  residues processed: 72
  average time/residue: 0.4073
  time to fit residues: 30.7948
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  436 ASP
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:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.5538

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.111267 restraints weight = 4973.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.69
r_work: 0.3111 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4327  Z= 0.111
  Angle     :  0.545   8.181   5907  Z= 0.270
  Chirality :  0.039   0.130    669
  Planarity :  0.004   0.047    722
  Dihedral  :  4.340  28.883    571
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.83 %
    Favored  : 81.80 %
  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:  0.90 (0.37), residues: 524
  helix:  1.09 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.44 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 615 
 TYR   0.015   0.001   TYR A 115 
 PHE   0.011   0.001   PHE A  76 
 TRP   0.009   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 4326)
  covalent geometry    : angle       0.54466 /  0.27 ( 5905)
  SS BOND              : bond        0.00039 /  0.02 (    1)
  SS BOND              : angle       0.14612 /  0.07 (    2)
  hydrogen bonds       : bond        0.03509 /  2.21 (  246)
  hydrogen bonds       : angle       4.21408 /  2.80 (  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
  80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  116 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8199 (ttm)
REVERT: A  226 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7839 (mt0)
REVERT: A  534 PHE cc_start: 0.7940 (t80) cc_final: 0.7592 (t80)
REVERT: A  593 TYR cc_start: 0.8071 (m-80) cc_final: 0.7813 (m-80)
REVERT: A  608 GLU cc_start: 0.6746 (mp0) cc_final: 0.6408 (pm20)
  outliers start: 15
  outliers final: 5
  residues processed: 74
  average time/residue: 0.3723
  time to fit residues: 28.8433
Evaluate side-chains
  68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  116 MET
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  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:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111012 restraints weight = 4884.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.65
r_work: 0.3094 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3323

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= 0.120
  Angle     :  0.554   9.109   5907  Z= 0.274
  Chirality :  0.040   0.133    669
  Planarity :  0.004   0.047    722
  Dihedral  :  4.309  29.348    571
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.40 %
    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:  1.05 (0.37), residues: 524
  helix:  1.19 (0.27), residues: 369
  sheet:  None (None), residues: 0
  loop : -0.34 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 295 
 TYR   0.017   0.001   TYR A 115 
 PHE   0.011   0.001   PHE A  76 
 TRP   0.010   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 4326)
  covalent geometry    : angle       0.55363 /  0.27 ( 5905)
  SS BOND              : bond        0.00017 /  0.01 (    1)
  SS BOND              : angle       0.15782 /  0.08 (    2)
  hydrogen bonds       : bond        0.03583 /  2.25 (  246)
  hydrogen bonds       : angle       4.21497 /  2.80 (  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
  74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7895 (mt0)
REVERT: A  336 ASN cc_start: 0.8331 (t0) cc_final: 0.8045 (t0)
REVERT: A  534 PHE cc_start: 0.7917 (t80) cc_final: 0.7552 (t80)
REVERT: A  593 TYR cc_start: 0.8106 (m-80) cc_final: 0.7835 (m-80)
REVERT: A  608 GLU cc_start: 0.6788 (mp0) cc_final: 0.6443 (pm20)
  outliers start: 11
  outliers final: 5
  residues processed: 69
  average time/residue: 0.4040
  time to fit residues: 29.1229
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  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:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.109685 restraints weight = 4936.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.69
r_work: 0.3072 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.3310

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= 0.139
  Angle     :  0.577  10.367   5907  Z= 0.286
  Chirality :  0.041   0.141    669
  Planarity :  0.004   0.048    722
  Dihedral  :  4.375  29.487    571
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.85 %
    Favored  : 80.67 %
  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:  1.03 (0.37), residues: 524
  helix:  1.18 (0.27), residues: 366
  sheet:  None (None), residues: 0
  loop : -0.35 (0.50), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 615 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.011   0.001   PHE A  76 
 TRP   0.012   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 4326)
  covalent geometry    : angle       0.57704 /  0.29 ( 5905)
  SS BOND              : bond        0.00024 /  0.01 (    1)
  SS BOND              : angle       0.17725 /  0.10 (    2)
  hydrogen bonds       : bond        0.03772 /  2.37 (  246)
  hydrogen bonds       : angle       4.27597 /  2.84 (  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  : 0.154 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7882 (mt0)
REVERT: A  336 ASN cc_start: 0.8346 (t0) cc_final: 0.8089 (t0)
REVERT: A  534 PHE cc_start: 0.7936 (t80) cc_final: 0.7564 (t80)
REVERT: A  593 TYR cc_start: 0.8122 (m-80) cc_final: 0.7817 (m-80)
REVERT: A  608 GLU cc_start: 0.6839 (mp0) cc_final: 0.6487 (pm20)
  outliers start: 11
  outliers final: 6
  residues processed: 69
  average time/residue: 0.3655
  time to fit residues: 26.5509
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  : 0.157 
-------------------------------------------------------------------------------
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 2 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 49 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.111346 restraints weight = 4888.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.67
r_work: 0.3098 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3412

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= 0.115
  Angle     :  0.557  11.546   5907  Z= 0.273
  Chirality :  0.039   0.129    669
  Planarity :  0.004   0.046    722
  Dihedral  :  4.268  29.184    571
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.53 %
    Favored  : 80.67 %
  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:  1.22 (0.37), residues: 524
  helix:  1.28 (0.27), residues: 370
  sheet:  None (None), residues: 0
  loop : -0.21 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 615 
 TYR   0.016   0.001   TYR A 115 
 PHE   0.010   0.001   PHE A  76 
 TRP   0.010   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.11 ( 4326)
  covalent geometry    : angle       0.55704 /  0.27 ( 5905)
  SS BOND              : bond        0.00002 /  0.00 (    1)
  SS BOND              : angle       0.14517 /  0.07 (    2)
  hydrogen bonds       : bond        0.03495 /  2.20 (  246)
  hydrogen bonds       : angle       4.18918 /  2.78 (  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
  71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7864 (mt0)
REVERT: A  336 ASN cc_start: 0.8308 (t0) cc_final: 0.8058 (t0)
REVERT: A  534 PHE cc_start: 0.7922 (t80) cc_final: 0.7584 (t80)
REVERT: A  593 TYR cc_start: 0.8149 (m-80) cc_final: 0.7927 (m-10)
REVERT: A  608 GLU cc_start: 0.6840 (mp0) cc_final: 0.6525 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.3597
  time to fit residues: 25.7093
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  : 0.147 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0370
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.136032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.112119 restraints weight = 4859.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.67
r_work: 0.3124 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.3495

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= 0.107
  Angle     :  0.545  11.418   5907  Z= 0.267
  Chirality :  0.039   0.122    669
  Planarity :  0.004   0.044    722
  Dihedral  :  4.155  29.164    571
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.98 %
    Favored  : 80.67 %
  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:  1.41 (0.37), residues: 524
  helix:  1.43 (0.27), residues: 371
  sheet:  None (None), residues: 0
  loop : -0.15 (0.52), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 615 
 TYR   0.014   0.001   TYR A 115 
 PHE   0.010   0.001   PHE A  76 
 TRP   0.009   0.001   TRP A 132 
 HIS   0.004   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 4326)
  covalent geometry    : angle       0.54529 /  0.27 ( 5905)
  SS BOND              : bond        0.00004 /  0.00 (    1)
  SS BOND              : angle       0.23216 /  0.12 (    2)
  hydrogen bonds       : bond        0.03352 /  2.11 (  246)
  hydrogen bonds       : angle       4.12196 /  2.73 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1547.57 seconds
wall clock time: 27 minutes 7.06 seconds (1627.06 seconds total)