Starting phenix.real_space_refine
on Tue Feb  3 16:26:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kxw_62630/02_2026/9kxw_62630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kxw_62630/02_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_62630/02_2026/9kxw_62630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kxw_62630/02_2026/9kxw_62630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kxw_62630/02_2026/9kxw_62630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kxw_62630/02_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-2.0-5952/lib/python3.9/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, 15
          Unusual residues: {' NA': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 1.32, 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: 0.46
  Conformation dependent library (CDL) restraints added in 424.9 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: 0.16
  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: 0.75

  Time building geometry restraints manager: 0.61 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 2.470
  nonbonded pdb=" O   GLY A  47 "
            pdb="NA    NA A 702 "
     model   vdw
     2.220 2.470
  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 2.470
  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:             0.100
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.100
  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:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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
  covalent geometry    : bond        0.01478 ( 5132)
  covalent geometry    : angle       1.80293 ( 7006)
  SS BOND              : bond        0.01427 (    2)
  SS BOND              : angle       0.94924 (    4)
  hydrogen bonds       : bond        0.23318 (  310)
  hydrogen bonds       : angle       8.89058 (  912)
  link_BETA1-4         : bond        0.00305 (    1)
  link_BETA1-4         : angle       0.55311 (    3)
  link_NAG-ASN         : bond        0.00465 (    2)
  link_NAG-ASN         : angle       8.55343 (    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  : 0.192 
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: 0.5075
  time to fit residues: 66.7116
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  : 0.197 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3522 r_free = 0.3522 target = 0.133490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110729 restraints weight = 5856.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.69
r_work: 0.3142 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2287

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= 0.156
  Angle     :  0.645  10.058   7019  Z= 0.332
  Chirality :  0.043   0.357    815
  Planarity :  0.005   0.042    857
  Dihedral  :  7.050  58.576    746
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 11.86 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.33), residues: 616
  helix:  0.69 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -0.77 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 513 
 TYR   0.021   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 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5132)
  covalent geometry    : angle       0.62354 ( 7006)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       1.87831 (    4)
  hydrogen bonds       : bond        0.05665 (  310)
  hydrogen bonds       : angle       5.23535 (  912)
  link_BETA1-4         : bond        0.00138 (    1)
  link_BETA1-4         : angle       0.66798 (    3)
  link_NAG-ASN         : bond        0.00678 (    2)
  link_NAG-ASN         : angle       5.43162 (    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
  102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8680 (tt)
REVERT: A  228 THR cc_start: 0.8607 (m) cc_final: 0.8364 (p)
REVERT: A  266 ASP cc_start: 0.6788 (t0) cc_final: 0.6459 (p0)
REVERT: A  452 LYS cc_start: 0.6813 (mttt) cc_final: 0.6489 (tmtt)
REVERT: A  455 LYS cc_start: 0.7547 (mttt) cc_final: 0.7304 (tttt)
REVERT: A  485 LEU cc_start: 0.7802 (mt) cc_final: 0.7395 (tp)
REVERT: A  519 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8239 (tt0)
REVERT: A  541 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8118 (mt)
REVERT: A  580 ASN cc_start: 0.7230 (p0) cc_final: 0.7004 (m-40)
REVERT: A  588 ILE cc_start: 0.8684 (mt) cc_final: 0.8461 (mm)
  outliers start: 21
  outliers final: 2
  residues processed: 95
  average time/residue: 0.5256
  time to fit residues: 52.0207
Evaluate side-chains
  69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  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  519 GLU
Chi-restraints excluded: chain A residue  541 LEU
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:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3518 r_free = 0.3518 target = 0.133088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.111185 restraints weight = 5842.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.66
r_work: 0.3135 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5137  Z= 0.134
  Angle     :  0.604   9.056   7019  Z= 0.306
  Chirality :  0.041   0.343    815
  Planarity :  0.005   0.033    857
  Dihedral  :  4.848  38.264    729
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.50 %
    Favored  : 83.03 %
  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:  1.10 (0.34), residues: 616
  helix:  1.33 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -0.48 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  57 
 TYR   0.020   0.002   TYR A 322 
 PHE   0.015   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
  covalent geometry    : bond        0.00288 ( 5132)
  covalent geometry    : angle       0.58725 ( 7006)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       1.30931 (    4)
  hydrogen bonds       : bond        0.04958 (  310)
  hydrogen bonds       : angle       4.91602 (  912)
  link_BETA1-4         : bond        0.00473 (    1)
  link_BETA1-4         : angle       0.50385 (    3)
  link_NAG-ASN         : bond        0.00665 (    2)
  link_NAG-ASN         : angle       4.74110 (    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
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8719 (tt)
REVERT: A  228 THR cc_start: 0.8601 (m) cc_final: 0.8352 (p)
REVERT: A  266 ASP cc_start: 0.6693 (t0) cc_final: 0.6459 (p0)
REVERT: A  332 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8092 (mtm180)
REVERT: A  452 LYS cc_start: 0.6919 (mttt) cc_final: 0.6544 (tmtt)
REVERT: A  455 LYS cc_start: 0.7476 (mttt) cc_final: 0.7253 (tttt)
REVERT: A  485 LEU cc_start: 0.7769 (mt) cc_final: 0.7415 (tt)
REVERT: A  580 ASN cc_start: 0.7254 (p0) cc_final: 0.7030 (m-40)
  outliers start: 19
  outliers final: 5
  residues processed: 88
  average time/residue: 0.5404
  time to fit residues: 49.6359
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  419 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
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:    7.9990
   chunk 48 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3443 r_free = 0.3443 target = 0.126883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.104732 restraints weight = 5888.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.65
r_work: 0.3041 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5137  Z= 0.185
  Angle     :  0.650  10.115   7019  Z= 0.329
  Chirality :  0.044   0.369    815
  Planarity :  0.005   0.041    857
  Dihedral  :  5.158  39.295    729
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.96 %
    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:  1.21 (0.34), residues: 616
  helix:  1.43 (0.26), residues: 421
  sheet:  None (None), residues: 0
  loop : -0.50 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  57 
 TYR   0.023   0.002   TYR A 322 
 PHE   0.020   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
  covalent geometry    : bond        0.00436 ( 5132)
  covalent geometry    : angle       0.63064 ( 7006)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       1.23772 (    4)
  hydrogen bonds       : bond        0.05546 (  310)
  hydrogen bonds       : angle       4.99482 (  912)
  link_BETA1-4         : bond        0.00274 (    1)
  link_BETA1-4         : angle       0.53857 (    3)
  link_NAG-ASN         : bond        0.00552 (    2)
  link_NAG-ASN         : angle       5.42495 (    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
  89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8648 (tt)
REVERT: A  228 THR cc_start: 0.8689 (m) cc_final: 0.8395 (p)
REVERT: A  266 ASP cc_start: 0.6818 (t0) cc_final: 0.6577 (p0)
REVERT: A  332 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8058 (mtm180)
REVERT: A  452 LYS cc_start: 0.6896 (mttt) cc_final: 0.6439 (tmtt)
REVERT: A  455 LYS cc_start: 0.7413 (mttt) cc_final: 0.7189 (tttt)
REVERT: A  485 LEU cc_start: 0.7658 (mt) cc_final: 0.7453 (tt)
REVERT: A  580 ASN cc_start: 0.7414 (p0) cc_final: 0.7079 (m-40)
REVERT: A  604 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7495 (mmtt)
  outliers start: 20
  outliers final: 9
  residues processed: 83
  average time/residue: 0.5276
  time to fit residues: 45.5899
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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  573 SER
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:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3508 r_free = 0.3508 target = 0.132020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.110353 restraints weight = 5937.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.64
r_work: 0.3120 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3403

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= 0.119
  Angle     :  0.583   8.690   7019  Z= 0.290
  Chirality :  0.040   0.329    815
  Planarity :  0.004   0.030    857
  Dihedral  :  4.817  38.389    729
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.33 %
    Favored  : 81.20 %
  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:  1.50 (0.35), residues: 616
  helix:  1.66 (0.26), residues: 422
  sheet:  None (None), residues: 0
  loop : -0.42 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.020   0.001   TYR A 322 
 PHE   0.010   0.001   PHE A 421 
 TRP   0.010   0.001   TRP A 205 
 HIS   0.003   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5132)
  covalent geometry    : angle       0.56770 ( 7006)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.75192 (    4)
  hydrogen bonds       : bond        0.04561 (  310)
  hydrogen bonds       : angle       4.75960 (  912)
  link_BETA1-4         : bond        0.00439 (    1)
  link_BETA1-4         : angle       0.85992 (    3)
  link_NAG-ASN         : bond        0.00700 (    2)
  link_NAG-ASN         : angle       4.54621 (    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
  87 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8653 (tt)
REVERT: A  228 THR cc_start: 0.8583 (m) cc_final: 0.8315 (p)
REVERT: A  266 ASP cc_start: 0.6731 (t0) cc_final: 0.6470 (p0)
REVERT: A  332 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8068 (mtm180)
REVERT: A  452 LYS cc_start: 0.6954 (mttt) cc_final: 0.6478 (tmtt)
REVERT: A  455 LYS cc_start: 0.7411 (mttt) cc_final: 0.7201 (tttt)
REVERT: A  580 ASN cc_start: 0.7273 (p0) cc_final: 0.7024 (m-40)
REVERT: A  604 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7564 (mmtt)
  outliers start: 19
  outliers final: 6
  residues processed: 81
  average time/residue: 0.5451
  time to fit residues: 46.0608
Evaluate side-chains
  70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  101 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  573 SER
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:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0060
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.133407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111782 restraints weight = 5995.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.66
r_work: 0.3113 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5137  Z= 0.113
  Angle     :  0.563   8.031   7019  Z= 0.279
  Chirality :  0.039   0.317    815
  Planarity :  0.004   0.028    857
  Dihedral  :  4.627  38.277    729
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.24 %
    Favored  : 81.20 %
  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:  1.64 (0.35), residues: 616
  helix:  1.77 (0.26), residues: 422
  sheet:  None (None), residues: 0
  loop : -0.40 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  57 
 TYR   0.019   0.001   TYR A 322 
 PHE   0.019   0.001   PHE A 549 
 TRP   0.009   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 5132)
  covalent geometry    : angle       0.54982 ( 7006)
  SS BOND              : bond        0.00083 (    2)
  SS BOND              : angle       0.55958 (    4)
  hydrogen bonds       : bond        0.04227 (  310)
  hydrogen bonds       : angle       4.64729 (  912)
  link_BETA1-4         : bond        0.00479 (    1)
  link_BETA1-4         : angle       0.94558 (    3)
  link_NAG-ASN         : bond        0.00691 (    2)
  link_NAG-ASN         : angle       4.15566 (    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
  83 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8437 (tmt-80) cc_final: 0.8107 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8644 (tt)
REVERT: A  228 THR cc_start: 0.8438 (m) cc_final: 0.8192 (p)
REVERT: A  266 ASP cc_start: 0.6692 (t0) cc_final: 0.6468 (p0)
REVERT: A  332 ARG cc_start: 0.8405 (mtm110) cc_final: 0.8063 (mtm180)
REVERT: A  452 LYS cc_start: 0.6897 (mttt) cc_final: 0.6460 (tmtt)
REVERT: A  455 LYS cc_start: 0.7382 (mttt) cc_final: 0.7143 (ttmt)
REVERT: A  604 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7663 (mmtt)
  outliers start: 14
  outliers final: 7
  residues processed: 78
  average time/residue: 0.5388
  time to fit residues: 43.8359
Evaluate side-chains
  73 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  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  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:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.131969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.110148 restraints weight = 5921.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.66
r_work: 0.3140 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3677

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= 0.119
  Angle     :  0.578   8.068   7019  Z= 0.285
  Chirality :  0.040   0.320    815
  Planarity :  0.004   0.026    857
  Dihedral  :  4.555  38.298    729
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.79 %
    Favored  : 80.84 %
  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:  1.75 (0.35), residues: 616
  helix:  1.86 (0.26), residues: 423
  sheet:  None (None), residues: 0
  loop : -0.35 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.019   0.001   TYR A 322 
 PHE   0.012   0.001   PHE A 549 
 TRP   0.011   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5132)
  covalent geometry    : angle       0.56490 ( 7006)
  SS BOND              : bond        0.00041 (    2)
  SS BOND              : angle       0.88695 (    4)
  hydrogen bonds       : bond        0.04315 (  310)
  hydrogen bonds       : angle       4.62846 (  912)
  link_BETA1-4         : bond        0.00455 (    1)
  link_BETA1-4         : angle       0.87846 (    3)
  link_NAG-ASN         : bond        0.00607 (    2)
  link_NAG-ASN         : angle       4.18839 (    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
  80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8438 (tmt-80) cc_final: 0.8210 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8662 (tt)
REVERT: A  332 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7936 (mtm180)
REVERT: A  452 LYS cc_start: 0.6941 (mttt) cc_final: 0.6486 (tmtt)
REVERT: A  604 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7683 (mmtt)
REVERT: B  759 ILE cc_start: 0.8429 (mt) cc_final: 0.8228 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 76
  average time/residue: 0.5567
  time to fit residues: 44.1276
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  423 MET
Chi-restraints excluded: chain A residue  443 LEU
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:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3518 r_free = 0.3518 target = 0.132648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.111141 restraints weight = 5910.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.65
r_work: 0.3126 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3795

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= 0.117
  Angle     :  0.572   7.813   7019  Z= 0.283
  Chirality :  0.040   0.313    815
  Planarity :  0.004   0.066    857
  Dihedral  :  4.225  31.382    727
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.42 %
    Favored  : 81.20 %
  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:  1.90 (0.35), residues: 616
  helix:  1.97 (0.26), residues: 424
  sheet:  None (None), residues: 0
  loop : -0.30 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.019   0.001   TYR A 322 
 PHE   0.014   0.001   PHE A 549 
 TRP   0.010   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5132)
  covalent geometry    : angle       0.55915 ( 7006)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.87549 (    4)
  hydrogen bonds       : bond        0.04216 (  310)
  hydrogen bonds       : angle       4.59887 (  912)
  link_BETA1-4         : bond        0.00415 (    1)
  link_BETA1-4         : angle       1.00521 (    3)
  link_NAG-ASN         : bond        0.00613 (    2)
  link_NAG-ASN         : angle       4.06385 (    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
  81 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8379 (tmt-80) cc_final: 0.8042 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8663 (tt)
REVERT: A  129 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7904 (t80)
REVERT: A  332 ARG cc_start: 0.8318 (mtm110) cc_final: 0.7923 (mtm180)
REVERT: A  452 LYS cc_start: 0.7021 (mttt) cc_final: 0.6543 (tmtt)
REVERT: A  604 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7671 (mmtt)
  outliers start: 13
  outliers final: 7
  residues processed: 77
  average time/residue: 0.4687
  time to fit residues: 37.8292
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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  129 TYR
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 A residue  604 LYS
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:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.110110 restraints weight = 5887.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.65
r_work: 0.3121 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3827

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= 0.127
  Angle     :  0.594   8.008   7019  Z= 0.293
  Chirality :  0.040   0.320    815
  Planarity :  0.005   0.066    857
  Dihedral  :  4.220  28.692    727
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.15 %
    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:  1.93 (0.35), residues: 616
  helix:  1.99 (0.26), residues: 424
  sheet:  None (None), residues: 0
  loop : -0.31 (0.45), residues: 192

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   0.015   0.001   PHE A 549 
 TRP   0.011   0.001   TRP A 195 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5132)
  covalent geometry    : angle       0.58076 ( 7006)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.97241 (    4)
  hydrogen bonds       : bond        0.04442 (  310)
  hydrogen bonds       : angle       4.63900 (  912)
  link_BETA1-4         : bond        0.00400 (    1)
  link_BETA1-4         : angle       0.90053 (    3)
  link_NAG-ASN         : bond        0.00561 (    2)
  link_NAG-ASN         : angle       4.19643 (    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
  79 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8372 (tmt-80) cc_final: 0.8089 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8702 (tt)
REVERT: A  256 THR cc_start: 0.7203 (m) cc_final: 0.6872 (m)
REVERT: A  332 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7922 (mtm180)
REVERT: A  452 LYS cc_start: 0.7040 (mttt) cc_final: 0.6536 (tmtt)
REVERT: A  604 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7673 (mmtt)
  outliers start: 12
  outliers final: 8
  residues processed: 76
  average time/residue: 0.5176
  time to fit residues: 41.0113
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  : 0.188 
-------------------------------------------------------------------------------
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  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain A residue  604 LYS
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:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0870
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3489 r_free = 0.3489 target = 0.130551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.108847 restraints weight = 5854.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.65
r_work: 0.3113 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3825

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= 0.146
  Angle     :  0.622   8.389   7019  Z= 0.309
  Chirality :  0.041   0.332    815
  Planarity :  0.005   0.064    857
  Dihedral  :  4.358  26.139    727
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.70 %
    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:  1.89 (0.35), residues: 616
  helix:  1.95 (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   0.004   0.000   ARG A 240 
 TYR   0.021   0.002   TYR A 322 
 PHE   0.015   0.002   PHE A 549 
 TRP   0.011   0.002   TRP A 205 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5132)
  covalent geometry    : angle       0.60733 ( 7006)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       1.07333 (    4)
  hydrogen bonds       : bond        0.04782 (  310)
  hydrogen bonds       : angle       4.71988 (  912)
  link_BETA1-4         : bond        0.00326 (    1)
  link_BETA1-4         : angle       0.89967 (    3)
  link_NAG-ASN         : bond        0.00503 (    2)
  link_NAG-ASN         : angle       4.47216 (    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
  78 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8401 (tmt-80) cc_final: 0.8090 (tmt-80)
REVERT: A   78 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8710 (tt)
REVERT: A  332 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7900 (mtm180)
REVERT: A  452 LYS cc_start: 0.7065 (mttt) cc_final: 0.6498 (tmtt)
  outliers start: 12
  outliers final: 8
  residues processed: 74
  average time/residue: 0.4598
  time to fit residues: 35.5947
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
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  423 MET
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  525 LYS
Chi-restraints excluded: chain A residue  575 LYS
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:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3485 r_free = 0.3485 target = 0.129681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.107364 restraints weight = 5871.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.69
r_work: 0.3081 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3861

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= 0.143
  Angle     :  0.615   8.448   7019  Z= 0.305
  Chirality :  0.041   0.331    815
  Planarity :  0.005   0.063    857
  Dihedral  :  4.358  25.222    727
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.52 %
    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:  1.88 (0.35), residues: 616
  helix:  1.96 (0.26), residues: 424
  sheet:  None (None), residues: 0
  loop : -0.32 (0.45), residues: 192

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   0.015   0.001   PHE A 549 
 TRP   0.011   0.002   TRP A 481 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5132)
  covalent geometry    : angle       0.60089 ( 7006)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       1.03967 (    4)
  hydrogen bonds       : bond        0.04750 (  310)
  hydrogen bonds       : angle       4.70842 (  912)
  link_BETA1-4         : bond        0.00339 (    1)
  link_BETA1-4         : angle       1.01487 (    3)
  link_NAG-ASN         : bond        0.00490 (    2)
  link_NAG-ASN         : angle       4.46611 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1759.81 seconds
wall clock time: 30 minutes 48.34 seconds (1848.34 seconds total)