Starting phenix.real_space_refine
on Thu Jul  2 01:02:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kxw_62630/07_2026/9kxw_62630.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     Na      1      4.78       5
     C    3309      2.51       5
     N     769      2.21       5
     O     883      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 4992
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4704
          Classifications: {'peptide': 592}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 29, 'TRANS': 562}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "B"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 245
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 14
          Ad-hoc single atom residues: {' NA': 1}
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.26
  Number of scatterers: 4992
  At special positions: 0
  Unit cell: (65.2935, 69.7202, 108.454, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     Na      1     11.00
     O     883      8.00
     N     769      7.00
     C    3309      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 153 " - pdb=" SG  CYS A 166 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 383 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 182 "
      " NAG C   1 " - " ASN A 258 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 115.4 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1156

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 1 sheets defined
      77.2% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 4.213A  pdb=" N   GLU A  25 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 50
      removed outlier: 3.845A  pdb=" N   TYR A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 57 through 65
      removed outlier: 3.564A  pdb=" N   GLN A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 81
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 99 through 108
    Processing helix  chain 'A' and resid 111 through 142
      removed outlier: 3.841A  pdb=" N   GLY A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 194 through 212
      removed outlier: 3.613A  pdb=" N   CYS A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 4.881A  pdb=" N   LYS A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ILE A 225 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 244
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.849A  pdb=" N   TRP A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 291
      removed outlier: 3.824A  pdb=" N   SER A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 348
      removed outlier: 3.520A  pdb=" N   SER A 303 " --> pdb=" O   CYS A 299 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 324 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 359
    Processing helix  chain 'A' and resid 360 through 365
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.523A  pdb=" N   THR A 408 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 447
      removed outlier: 3.804A  pdb=" N   VAL A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.882A  pdb=" N   LEU A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 475
    Processing helix  chain 'A' and resid 477 through 487
      removed outlier: 3.603A  pdb=" N   SER A 487 " --> pdb=" O   SER A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 508
    Processing helix  chain 'A' and resid 510 through 523
    Processing helix  chain 'A' and resid 527 through 536
    Processing helix  chain 'A' and resid 536 through 553
      removed outlier: 3.601A  pdb=" N   ILE A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 546 " --> pdb=" O   MET A 542 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE A 550 " --> pdb=" O   PHE A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 556
      No H-bonds generated for 'chain 'A' and resid 554 through 556'
    Processing helix  chain 'A' and resid 581 through 591
      removed outlier: 3.696A  pdb=" N   VAL A 585 " --> pdb=" O   TRP A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 609
      removed outlier: 5.391A  pdb=" N   ILE A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 3.736A  pdb=" N   ALA A 601 " --> pdb=" O   ILE A 597 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 608 " --> pdb=" O   LYS A 604 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   HIS A 609 " --> pdb=" O   LEU A 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 768
    Processing sheet with id=AA1, first strand: chain 'A' and resid 559 through 562
      removed outlier: 4.346A  pdb=" N   GLN A 574 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)

    310 hydrogen bonds defined for protein.
    912 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: 0.77

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 764
        1.29 -     1.43: 1463
        1.43 -     1.57: 2859
        1.57 -     1.71: 0
        1.71 -     1.85: 46
  Bond restraints: 5132
  Sorted by residual:
  bond pdb=" C   PRO A  59 "
       pdb=" O   PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.237  1.155  0.082 1.26e-02 6.30e+03 4.26e+01
  bond pdb=" C   PRO A 230 "
       pdb=" O   PRO A 230 "
    ideal  model  delta    sigma   weight residual
    1.237  1.160  0.077 1.26e-02 6.30e+03 3.74e+01
  bond pdb=" C   GLU A 501 "
       pdb=" O   GLU A 501 "
    ideal  model  delta    sigma   weight residual
    1.236  1.174  0.063 1.15e-02 7.56e+03 2.98e+01
  bond pdb=" C   SER A 288 "
       pdb=" O   SER A 288 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.061 1.15e-02 7.56e+03 2.83e+01
  bond pdb=" C   SER A 417 "
       pdb=" O   SER A 417 "
    ideal  model  delta    sigma   weight residual
    1.237  1.180  0.057 1.19e-02 7.06e+03 2.26e+01
  ... (remaining 5127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4622
        1.69 -     3.39: 1969
        3.39 -     5.08: 358
        5.08 -     6.77: 47
        6.77 -     8.47: 10
  Bond angle restraints: 7006
  Sorted by residual:
  angle pdb=" CA  ILE A 407 "
        pdb=" C   ILE A 407 "
        pdb=" O   ILE A 407 "
      ideal   model   delta    sigma   weight residual
     120.85  114.28    6.57 1.06e+00 8.90e-01 3.84e+01
  angle pdb=" CA  LEU A 286 "
        pdb=" C   LEU A 286 "
        pdb=" O   LEU A 286 "
      ideal   model   delta    sigma   weight residual
     120.55  114.66    5.89 1.06e+00 8.90e-01 3.08e+01
  angle pdb=" CA  THR A 235 "
        pdb=" C   THR A 235 "
        pdb=" O   THR A 235 "
      ideal   model   delta    sigma   weight residual
     120.90  115.25    5.65 1.03e+00 9.43e-01 3.01e+01
  angle pdb=" C   VAL A 506 "
        pdb=" CA  VAL A 506 "
        pdb=" CB  VAL A 506 "
      ideal   model   delta    sigma   weight residual
     110.91  116.18   -5.27 9.80e-01 1.04e+00 2.89e+01
  angle pdb=" N   VAL A 592 "
        pdb=" CA  VAL A 592 "
        pdb=" CB  VAL A 592 "
      ideal   model   delta    sigma   weight residual
     110.50  113.82   -3.32 6.30e-01 2.52e+00 2.78e+01
  ... (remaining 7001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 2681
       16.57 -    33.14: 234
       33.14 -    49.71: 50
       49.71 -    66.28: 20
       66.28 -    82.84: 3
  Dihedral angle restraints: 2988
    sinusoidal: 1186
      harmonic: 1802
  Sorted by residual:
  dihedral pdb=" CA  GLU A  28 "
           pdb=" C   GLU A  28 "
           pdb=" N   ALA A  29 "
           pdb=" CA  ALA A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLY A 284 "
           pdb=" C   GLY A 284 "
           pdb=" N   GLY A 285 "
           pdb=" CA  GLY A 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  TYR A 322 "
           pdb=" C   TYR A 322 "
           pdb=" N   SER A 323 "
           pdb=" CA  SER A 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.07   15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.167: 776
       0.167 -    0.334: 38
       0.334 -    0.501: 0
       0.501 -    0.668: 0
       0.668 -    0.835: 1
  Chirality restraints: 815
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-02 2.50e+03 4.58e+01
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 182 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.56   -0.84 2.00e-01 2.50e+01 1.74e+01
  chirality pdb=" CB  VAL A 592 "
            pdb=" CA  VAL A 592 "
            pdb=" CG1 VAL A 592 "
            pdb=" CG2 VAL A 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 812 not shown)

  Planarity restraints: 859
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 592 "    0.048 5.00e-02 4.00e+02   7.36e-02 8.67e+00
        pdb=" N   PRO A 593 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 240 "    0.253 9.50e-02 1.11e+02   1.13e-01 7.89e+00
        pdb=" NE  ARG A 240 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 240 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 240 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 240 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 153 "    0.041 5.00e-02 4.00e+02   6.53e-02 6.83e+00
        pdb=" N   PRO A 154 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 154 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 154 "    0.037 5.00e-02 4.00e+02
  ... (remaining 856 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 221
        2.73 -     3.27: 5655
        3.27 -     3.81: 8073
        3.81 -     4.36: 11346
        4.36 -     4.90: 17545
  Nonbonded interactions: 42840
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  50 "
            pdb="NA    NA A 702 "
     model   vdw
     2.184 3.210
  nonbonded pdb=" O   GLY A  47 "
            pdb="NA    NA A 702 "
     model   vdw
     2.220 3.210
  nonbonded pdb=" O   GLY A 395 "
            pdb=" N   GLY A 397 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" O   LEU A 427 "
            pdb="NA    NA A 702 "
     model   vdw
     2.398 3.210
  nonbonded pdb=" NZ  LYS A  38 "
            pdb=" OD1 ASN A 297 "
     model   vdw
     2.449 3.120
  ... (remaining 42835 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.240
  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:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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      :  0.015   0.082   5137  Z= 1.070
  Angle     :  1.819  16.947   7019  Z= 1.357
  Chirality :  0.094   0.835    815
  Planarity :  0.009   0.113    857
  Dihedral  : 13.865  82.844   1826
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.01 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  :  8.21 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.29), residues: 616
  helix: -1.87 (0.21), residues: 419
  sheet:  None (None), residues: 0
  loop : -1.87 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 328 
 TYR   0.024   0.003   TYR A 322 
 PHE   0.019   0.003   PHE A 327 
 TRP   0.020   0.005   TRP A 195 
 HIS   0.002   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01478 /  1.07 ( 5132)
  covalent geometry    : angle       1.80293 /  1.36 ( 7006)
  SS BOND              : bond        0.01427 /  0.75 (    2)
  SS BOND              : angle       0.94924 /  0.56 (    4)
  hydrogen bonds       : bond        0.23318 / 15.45 (  310)
  hydrogen bonds       : angle       8.89058 /  6.39 (  912)
  link_BETA1-4         : bond        0.00305 /  0.16 (    1)
  link_BETA1-4         : angle       0.55311 /  0.28 (    3)
  link_NAG-ASN         : bond        0.00465 /  0.23 (    2)
  link_NAG-ASN         : angle       8.55343 /  4.11 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7860 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8397 (tp) cc_final: 0.8143 (tt)
REVERT: A   98 ARG cc_start: 0.7619 (mtt-85) cc_final: 0.7304 (mmm-85)
REVERT: A  170 SER cc_start: 0.8630 (t) cc_final: 0.8337 (p)
REVERT: A  217 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8036 (tt0)
REVERT: A  228 THR cc_start: 0.8544 (m) cc_final: 0.7946 (p)
REVERT: A  245 LYS cc_start: 0.7350 (tptp) cc_final: 0.7009 (mmpt)
REVERT: A  266 ASP cc_start: 0.7081 (t0) cc_final: 0.6816 (p0)
REVERT: A  310 ASN cc_start: 0.8252 (t0) cc_final: 0.8005 (t0)
REVERT: A  363 MET cc_start: 0.7928 (mmt) cc_final: 0.7566 (tpp)
REVERT: A  384 ASP cc_start: 0.6844 (m-30) cc_final: 0.6342 (p0)
REVERT: A  452 LYS cc_start: 0.6482 (mttt) cc_final: 0.6178 (tmtt)
REVERT: A  455 LYS cc_start: 0.7368 (mttt) cc_final: 0.6881 (tptt)
REVERT: A  485 LEU cc_start: 0.7685 (mt) cc_final: 0.7228 (tp)
REVERT: A  495 LEU cc_start: 0.7947 (mt) cc_final: 0.7655 (mt)
REVERT: A  516 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6954 (mttp)
REVERT: A  547 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6532 (mt)
REVERT: A  580 ASN cc_start: 0.7286 (p0) cc_final: 0.6849 (m-40)
  outliers start: 24
  outliers final: 5
  residues processed: 126
  average time/residue: 0.4523
  time to fit residues: 59.5581
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   37 ASN
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  516 LYS
Chi-restraints excluded: chain A residue  547 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 GLN
A 249 ASN
A 340 ASN
A 524 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.133273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.110562 restraints weight = 5875.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.68
r_work: 0.3128 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5137  Z= 0.159
  Angle     :  0.654  10.201   7019  Z= 0.337
  Chirality :  0.043   0.362    815
  Planarity :  0.005   0.040    857
  Dihedral  :  7.052  58.129    746
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 12.04 %
    Favored  : 84.12 %
  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:  0.24 (0.33), residues: 616
  helix:  0.64 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.70 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 513 
 TYR   0.020   0.002   TYR A 322 
 PHE   0.017   0.002   PHE A 514 
 TRP   0.014   0.002   TRP A 195 
 HIS   0.002   0.001   HIS A  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.16 ( 5132)
  covalent geometry    : angle       0.63376 /  0.33 ( 7006)
  SS BOND              : bond        0.00237 /  0.12 (    2)
  SS BOND              : angle       1.56783 /  0.83 (    4)
  hydrogen bonds       : bond        0.05644 /  3.72 (  310)
  hydrogen bonds       : angle       5.28335 /  3.66 (  912)
  link_BETA1-4         : bond        0.00071 /  0.04 (    1)
  link_BETA1-4         : angle       0.63908 /  0.36 (    3)
  link_NAG-ASN         : bond        0.00627 /  0.33 (    2)
  link_NAG-ASN         : angle       5.49893 /  2.77 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8679 (tt)
REVERT: A  228 THR cc_start: 0.8640 (m) cc_final: 0.8399 (p)
REVERT: A  266 ASP cc_start: 0.6820 (t0) cc_final: 0.6460 (p0)
REVERT: A  332 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8082 (mtm180)
REVERT: A  452 LYS cc_start: 0.6815 (mttt) cc_final: 0.6492 (tmtt)
REVERT: A  455 LYS cc_start: 0.7542 (mttt) cc_final: 0.7304 (tttt)
REVERT: A  485 LEU cc_start: 0.7815 (mt) cc_final: 0.7405 (tp)
REVERT: A  519 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8231 (tt0)
REVERT: A  541 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8115 (mt)
REVERT: A  580 ASN cc_start: 0.7238 (p0) cc_final: 0.7023 (m-40)
REVERT: A  588 ILE cc_start: 0.8683 (mt) cc_final: 0.8454 (mm)
  outliers start: 21
  outliers final: 4
  residues processed: 94
  average time/residue: 0.4657
  time to fit residues: 45.7696
Evaluate side-chains
  69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  519 GLU
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  589 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
A 310 ASN
A 331 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.132266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.110323 restraints weight = 5856.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.66
r_work: 0.3104 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5137  Z= 0.137
  Angle     :  0.608   9.207   7019  Z= 0.308
  Chirality :  0.041   0.343    815
  Planarity :  0.005   0.033    857
  Dihedral  :  5.316  45.336    731
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 13.50 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.34), residues: 616
  helix:  1.30 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -0.45 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.021   0.002   TYR A 322 
 PHE   0.014   0.002   PHE A 549 
 TRP   0.013   0.002   TRP A 205 
 HIS   0.003   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 5132)
  covalent geometry    : angle       0.59167 /  0.30 ( 7006)
  SS BOND              : bond        0.00056 /  0.03 (    2)
  SS BOND              : angle       1.25086 /  0.68 (    4)
  hydrogen bonds       : bond        0.04973 /  3.28 (  310)
  hydrogen bonds       : angle       4.93459 /  3.42 (  912)
  link_BETA1-4         : bond        0.00417 /  0.22 (    1)
  link_BETA1-4         : angle       0.43124 /  0.23 (    3)
  link_NAG-ASN         : bond        0.00643 /  0.34 (    2)
  link_NAG-ASN         : angle       4.80212 /  2.44 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: A  228 THR cc_start: 0.8594 (m) cc_final: 0.8341 (p)
REVERT: A  266 ASP cc_start: 0.6726 (t0) cc_final: 0.6457 (p0)
REVERT: A  332 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8097 (mtm180)
REVERT: A  452 LYS cc_start: 0.6855 (mttt) cc_final: 0.6513 (tmtt)
REVERT: A  455 LYS cc_start: 0.7483 (mttt) cc_final: 0.7252 (tttt)
REVERT: A  485 LEU cc_start: 0.7817 (mt) cc_final: 0.7489 (tt)
REVERT: A  580 ASN cc_start: 0.7239 (p0) cc_final: 0.7012 (m-40)
  outliers start: 22
  outliers final: 4
  residues processed: 90
  average time/residue: 0.4460
  time to fit residues: 42.0097
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  525 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN
A 531 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.126515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.104447 restraints weight = 5913.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.65
r_work: 0.3078 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5137  Z= 0.177
  Angle     :  0.647  10.034   7019  Z= 0.325
  Chirality :  0.043   0.367    815
  Planarity :  0.005   0.040    857
  Dihedral  :  5.129  39.053    729
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.78 %
    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:  1.19 (0.34), residues: 616
  helix:  1.40 (0.26), residues: 421
  sheet:  None (None), residues: 0
  loop : -0.48 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  57 
 TYR   0.023   0.002   TYR A 322 
 PHE   0.019   0.002   PHE A 549 
 TRP   0.014   0.002   TRP A 205 
 HIS   0.004   0.001   HIS A  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.18 ( 5132)
  covalent geometry    : angle       0.62755 /  0.32 ( 7006)
  SS BOND              : bond        0.00048 /  0.02 (    2)
  SS BOND              : angle       1.21891 /  0.67 (    4)
  hydrogen bonds       : bond        0.05426 /  3.59 (  310)
  hydrogen bonds       : angle       4.98073 /  3.47 (  912)
  link_BETA1-4         : bond        0.00321 /  0.17 (    1)
  link_BETA1-4         : angle       0.47657 /  0.27 (    3)
  link_NAG-ASN         : bond        0.00549 /  0.29 (    2)
  link_NAG-ASN         : angle       5.37738 /  2.75 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8649 (tt)
REVERT: A  266 ASP cc_start: 0.6847 (t0) cc_final: 0.6612 (p0)
REVERT: A  332 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8045 (mtm180)
REVERT: A  452 LYS cc_start: 0.6899 (mttt) cc_final: 0.6445 (tmtt)
REVERT: A  455 LYS cc_start: 0.7401 (mttt) cc_final: 0.7181 (tttt)
REVERT: A  485 LEU cc_start: 0.7651 (mt) cc_final: 0.7445 (tt)
REVERT: A  580 ASN cc_start: 0.7406 (p0) cc_final: 0.7073 (m-40)
REVERT: A  604 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7578 (mmtt)
  outliers start: 20
  outliers final: 8
  residues processed: 80
  average time/residue: 0.4717
  time to fit residues: 39.4960
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  604 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 HIS
A 293 ASN
A 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.133042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111546 restraints weight = 5944.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.65
r_work: 0.3138 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5137  Z= 0.114
  Angle     :  0.565   8.202   7019  Z= 0.282
  Chirality :  0.040   0.316    815
  Planarity :  0.004   0.031    857
  Dihedral  :  4.701  38.060    729
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.88 %
    Favored  : 81.39 %
  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:  1.54 (0.35), residues: 616
  helix:  1.68 (0.26), residues: 422
  sheet:  None (None), residues: 0
  loop : -0.38 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  57 
 TYR   0.019   0.001   TYR A 322 
 PHE   0.009   0.001   PHE A 514 
 TRP   0.010   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 5132)
  covalent geometry    : angle       0.55104 /  0.28 ( 7006)
  SS BOND              : bond        0.00145 /  0.08 (    2)
  SS BOND              : angle       0.77493 /  0.41 (    4)
  hydrogen bonds       : bond        0.04270 /  2.83 (  310)
  hydrogen bonds       : angle       4.68315 /  3.27 (  912)
  link_BETA1-4         : bond        0.00428 /  0.23 (    1)
  link_BETA1-4         : angle       1.13969 /  0.56 (    3)
  link_NAG-ASN         : bond        0.00773 /  0.41 (    2)
  link_NAG-ASN         : angle       4.22095 /  2.15 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (tt)
REVERT: A  228 THR cc_start: 0.8426 (m) cc_final: 0.8179 (p)
REVERT: A  266 ASP cc_start: 0.6728 (t0) cc_final: 0.6435 (p0)
REVERT: A  332 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7949 (mtm180)
REVERT: A  452 LYS cc_start: 0.6889 (mttt) cc_final: 0.6461 (tmtt)
REVERT: A  455 LYS cc_start: 0.7383 (mttt) cc_final: 0.7164 (tttt)
REVERT: A  485 LEU cc_start: 0.7614 (mt) cc_final: 0.7372 (tt)
REVERT: A  604 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7573 (mmtt)
  outliers start: 15
  outliers final: 3
  residues processed: 79
  average time/residue: 0.4132
  time to fit residues: 34.0945
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  604 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 57 optimal weight:    0.0070
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.1804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.131047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.109363 restraints weight = 6000.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.67
r_work: 0.3079 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5137  Z= 0.124
  Angle     :  0.587   8.368   7019  Z= 0.290
  Chirality :  0.040   0.329    815
  Planarity :  0.004   0.028    857
  Dihedral  :  4.670  38.423    729
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.88 %
    Favored  : 81.39 %
  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:  1.57 (0.35), residues: 616
  helix:  1.72 (0.26), residues: 422
  sheet:  None (None), residues: 0
  loop : -0.43 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.020   0.001   TYR A 322 
 PHE   0.018   0.001   PHE A 549 
 TRP   0.011   0.001   TRP A 205 
 HIS   0.003   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 5132)
  covalent geometry    : angle       0.57282 /  0.29 ( 7006)
  SS BOND              : bond        0.00113 /  0.06 (    2)
  SS BOND              : angle       0.71546 /  0.37 (    4)
  hydrogen bonds       : bond        0.04446 /  2.95 (  310)
  hydrogen bonds       : angle       4.68574 /  3.28 (  912)
  link_BETA1-4         : bond        0.00381 /  0.20 (    1)
  link_BETA1-4         : angle       0.85889 /  0.44 (    3)
  link_NAG-ASN         : bond        0.00610 /  0.32 (    2)
  link_NAG-ASN         : angle       4.36203 /  2.23 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8467 (tmt-80) cc_final: 0.8178 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8636 (tt)
REVERT: A  332 ARG cc_start: 0.8329 (mtm110) cc_final: 0.7917 (mtm180)
REVERT: A  452 LYS cc_start: 0.6951 (mttt) cc_final: 0.6492 (tmtt)
REVERT: A  455 LYS cc_start: 0.7391 (mttt) cc_final: 0.7155 (ttmt)
REVERT: A  604 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7614 (mmtt)
  outliers start: 15
  outliers final: 8
  residues processed: 75
  average time/residue: 0.4327
  time to fit residues: 33.7569
Evaluate side-chains
  73 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain A residue  604 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.108053 restraints weight = 5936.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.65
r_work: 0.3064 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5137  Z= 0.139
  Angle     :  0.601   8.726   7019  Z= 0.298
  Chirality :  0.041   0.338    815
  Planarity :  0.004   0.030    857
  Dihedral  :  4.755  38.874    729
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.06 %
    Favored  : 80.66 %
  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:  1.62 (0.35), residues: 616
  helix:  1.73 (0.26), residues: 422
  sheet:  None (None), residues: 0
  loop : -0.32 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 240 
 TYR   0.021   0.002   TYR A 322 
 PHE   0.013   0.001   PHE A 549 
 TRP   0.011   0.002   TRP A 205 
 HIS   0.003   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 5132)
  covalent geometry    : angle       0.58567 /  0.29 ( 7006)
  SS BOND              : bond        0.00114 /  0.06 (    2)
  SS BOND              : angle       1.03635 /  0.54 (    4)
  hydrogen bonds       : bond        0.04726 /  3.13 (  310)
  hydrogen bonds       : angle       4.76172 /  3.34 (  912)
  link_BETA1-4         : bond        0.00368 /  0.19 (    1)
  link_BETA1-4         : angle       0.82490 /  0.43 (    3)
  link_NAG-ASN         : bond        0.00539 /  0.28 (    2)
  link_NAG-ASN         : angle       4.57039 /  2.34 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8437 (tmt-80) cc_final: 0.8201 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8675 (tt)
REVERT: A  240 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8203 (tpp-160)
REVERT: A  452 LYS cc_start: 0.7003 (mttt) cc_final: 0.6492 (tmtt)
REVERT: A  604 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (mmtt)
  outliers start: 18
  outliers final: 10
  residues processed: 81
  average time/residue: 0.4565
  time to fit residues: 38.6963
Evaluate side-chains
  77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain A residue  604 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN
A 444 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.105397 restraints weight = 5938.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.65
r_work: 0.3032 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5137  Z= 0.202
  Angle     :  0.675   9.909   7019  Z= 0.336
  Chirality :  0.044   0.381    815
  Planarity :  0.005   0.038    857
  Dihedral  :  5.178  38.691    729
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.06 %
    Favored  : 81.02 %
  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:  1.26 (0.34), residues: 616
  helix:  1.43 (0.26), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.49 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 240 
 TYR   0.023   0.002   TYR A 322 
 PHE   0.017   0.002   PHE A 421 
 TRP   0.013   0.002   TRP A 205 
 HIS   0.004   0.002   HIS A  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.20 ( 5132)
  covalent geometry    : angle       0.65578 /  0.33 ( 7006)
  SS BOND              : bond        0.00143 /  0.08 (    2)
  SS BOND              : angle       1.32388 /  0.70 (    4)
  hydrogen bonds       : bond        0.05581 /  3.70 (  310)
  hydrogen bonds       : angle       4.96223 /  3.48 (  912)
  link_BETA1-4         : bond        0.00295 /  0.16 (    1)
  link_BETA1-4         : angle       0.67506 /  0.37 (    3)
  link_NAG-ASN         : bond        0.00461 /  0.24 (    2)
  link_NAG-ASN         : angle       5.37994 /  2.75 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8727 (tt)
REVERT: A  228 THR cc_start: 0.8722 (m) cc_final: 0.8389 (p)
REVERT: A  332 ARG cc_start: 0.8358 (mtm110) cc_final: 0.8067 (mtm180)
REVERT: A  452 LYS cc_start: 0.7040 (mttt) cc_final: 0.6430 (tmtt)
  outliers start: 16
  outliers final: 12
  residues processed: 79
  average time/residue: 0.4776
  time to fit residues: 39.5054
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain B residue  763 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN
A 609 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.127596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.105367 restraints weight = 5840.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.66
r_work: 0.3061 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5137  Z= 0.160
  Angle     :  0.635   9.479   7019  Z= 0.315
  Chirality :  0.042   0.357    815
  Planarity :  0.004   0.031    857
  Dihedral  :  5.025  37.999    729
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.97 %
    Favored  : 80.11 %
  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:  1.39 (0.34), residues: 616
  helix:  1.54 (0.26), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.47 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.022   0.002   TYR A 322 
 PHE   0.025   0.002   PHE A 549 
 TRP   0.012   0.002   TRP A 205 
 HIS   0.004   0.002   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.16 ( 5132)
  covalent geometry    : angle       0.61757 /  0.31 ( 7006)
  SS BOND              : bond        0.00107 /  0.06 (    2)
  SS BOND              : angle       1.13712 /  0.60 (    4)
  hydrogen bonds       : bond        0.05097 /  3.38 (  310)
  hydrogen bonds       : angle       4.88132 /  3.43 (  912)
  link_BETA1-4         : bond        0.00332 /  0.17 (    1)
  link_BETA1-4         : angle       0.88742 /  0.46 (    3)
  link_NAG-ASN         : bond        0.00523 /  0.28 (    2)
  link_NAG-ASN         : angle       5.03444 /  2.57 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8686 (tt)
REVERT: A  332 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8064 (mtm180)
REVERT: A  452 LYS cc_start: 0.7074 (mttt) cc_final: 0.6454 (tmtt)
  outliers start: 16
  outliers final: 12
  residues processed: 78
  average time/residue: 0.4562
  time to fit residues: 37.2204
Evaluate side-chains
  77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain B residue  763 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0050
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.9196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 310 ASN
A 609 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108462 restraints weight = 5805.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.68
r_work: 0.3088 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5137  Z= 0.124
  Angle     :  0.599   8.311   7019  Z= 0.297
  Chirality :  0.040   0.317    815
  Planarity :  0.004   0.029    857
  Dihedral  :  4.753  38.335    729
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.07 %
    Favored  : 79.93 %
  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:  1.77 (0.35), residues: 616
  helix:  1.83 (0.26), residues: 424
  sheet:  None (None), residues: 0
  loop : -0.27 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  57 
 TYR   0.019   0.001   TYR A 322 
 PHE   0.013   0.001   PHE A 549 
 TRP   0.010   0.001   TRP A 205 
 HIS   0.005   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5132)
  covalent geometry    : angle       0.58538 /  0.29 ( 7006)
  SS BOND              : bond        0.00114 /  0.06 (    2)
  SS BOND              : angle       0.84309 /  0.44 (    4)
  hydrogen bonds       : bond        0.04358 /  2.90 (  310)
  hydrogen bonds       : angle       4.68252 /  3.29 (  912)
  link_BETA1-4         : bond        0.00433 /  0.23 (    1)
  link_BETA1-4         : angle       1.13997 /  0.57 (    3)
  link_NAG-ASN         : bond        0.00652 /  0.34 (    2)
  link_NAG-ASN         : angle       4.31054 /  2.19 (    6)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (tt)
REVERT: A  332 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8081 (mtm180)
REVERT: A  452 LYS cc_start: 0.7027 (mttt) cc_final: 0.6469 (tmtt)
REVERT: B  759 ILE cc_start: 0.8416 (mt) cc_final: 0.8201 (mm)
  outliers start: 11
  outliers final: 7
  residues processed: 71
  average time/residue: 0.4644
  time to fit residues: 34.5121
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain B residue  763 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 609 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107809 restraints weight = 5877.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.69
r_work: 0.3068 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5137  Z= 0.131
  Angle     :  0.598   8.471   7019  Z= 0.298
  Chirality :  0.040   0.331    815
  Planarity :  0.004   0.030    857
  Dihedral  :  4.732  38.746    729
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.88 %
    Favored  : 80.11 %
  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:  1.80 (0.35), residues: 616
  helix:  1.87 (0.26), residues: 424
  sheet:  None (None), residues: 0
  loop : -0.28 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  57 
 TYR   0.020   0.001   TYR A 322 
 PHE   0.014   0.001   PHE A 549 
 TRP   0.012   0.001   TRP A 205 
 HIS   0.005   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 5132)
  covalent geometry    : angle       0.58376 /  0.29 ( 7006)
  SS BOND              : bond        0.00051 /  0.03 (    2)
  SS BOND              : angle       0.93424 /  0.49 (    4)
  hydrogen bonds       : bond        0.04521 /  3.01 (  310)
  hydrogen bonds       : angle       4.68142 /  3.30 (  912)
  link_BETA1-4         : bond        0.00357 /  0.19 (    1)
  link_BETA1-4         : angle       1.04594 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00601 /  0.32 (    2)
  link_NAG-ASN         : angle       4.41996 /  2.25 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1564.56 seconds
wall clock time: 27 minutes 23.49 seconds (1643.49 seconds total)