Starting phenix.real_space_refine
on Fri Aug 22 16:51:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdq_14666/08_2025/7zdq_14666.map"
  }
  resolution = 3.2
  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=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4010      2.51       5
     N    1037      2.21       5
     O    1184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6264
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "B"
      Number of atoms: 1345
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 166, 1339
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 8, 'TRANS': 157}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 166, 1339
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 8, 'TRANS': 157}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1370
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.70, per 1000 atoms: 0.43
  Number of scatterers: 6264
  At special positions: 0
  Unit cell: (96.025, 98.53, 91.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1184      8.00
     N    1037      7.00
     C    4010      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A  53 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 461.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      58.7% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 37
      removed outlier: 3.543A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.827A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.566A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.538A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.608A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.986A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.692A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.687A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 386
    Processing helix  chain 'A' and resid 400 through 414
      removed outlier: 3.584A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.401A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.538A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 368 through 372
      removed outlier: 4.063A  pdb=" N   ALA B 372 " --> pdb=" O   TYR B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 411
      removed outlier: 4.268A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA B 411 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.948A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.521A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)

    317 hydrogen bonds defined for protein.
    907 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: 0.69

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2010
        1.35 -     1.47: 1677
        1.47 -     1.59: 2701
        1.59 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" C   GLU A 589 "
       pdb=" N   PRO A 590 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.36e-02 5.41e+03 2.31e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.86e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.71e+00
  bond pdb=" C5  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.33e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 8459
        1.34 -     2.67: 224
        2.67 -     4.01: 50
        4.01 -     5.34: 16
        5.34 -     6.68: 3
  Bond angle restraints: 8752
  Sorted by residual:
  angle pdb=" N   LEU A  39 "
        pdb=" CA  LEU A  39 "
        pdb=" C   LEU A  39 "
      ideal   model   delta    sigma   weight residual
     113.41  108.45    4.96 1.22e+00 6.72e-01 1.65e+01
  angle pdb=" N   ILE A 259 "
        pdb=" CA  ILE A 259 "
        pdb=" C   ILE A 259 "
      ideal   model   delta    sigma   weight residual
     113.20  109.47    3.73 9.60e-01 1.09e+00 1.51e+01
  angle pdb=" C   PRO A 389 "
        pdb=" N   PHE A 390 "
        pdb=" CA  PHE A 390 "
      ideal   model   delta    sigma   weight residual
     120.82  124.88   -4.06 1.50e+00 4.44e-01 7.34e+00
  angle pdb=" CA  ALA A 614 "
        pdb=" C   ALA A 614 "
        pdb=" N   ASP A 615 "
      ideal   model   delta    sigma   weight residual
     119.26  116.40    2.86 1.14e+00 7.69e-01 6.31e+00
  angle pdb=" C   ALA A 614 "
        pdb=" N   ASP A 615 "
        pdb=" CA  ASP A 615 "
      ideal   model   delta    sigma   weight residual
     121.70  126.14   -4.44 1.80e+00 3.09e-01 6.09e+00
  ... (remaining 8747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3432
       18.00 -    36.00: 313
       36.00 -    54.00: 57
       54.00 -    71.99: 18
       71.99 -    89.99: 11
  Dihedral angle restraints: 3831
    sinusoidal: 1587
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.70   67.30     1      1.00e+01 1.00e-02 5.90e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.22   36.22     1      1.00e+01 1.00e-02 1.85e+01
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 3828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 644
       0.035 -    0.070: 184
       0.070 -    0.105: 73
       0.105 -    0.140: 14
       0.140 -    0.175: 1
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CB  ILE B 410 "
            pdb=" CA  ILE B 410 "
            pdb=" CG1 ILE B 410 "
            pdb=" CG2 ILE B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 913 not shown)

  Planarity restraints: 1135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 345 "   -0.052 5.00e-02 4.00e+02   7.73e-02 9.55e+00
        pdb=" N   PRO A 346 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 171 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" CD  GLU A 171 "    0.027 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 171 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 171 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.026 5.00e-02 4.00e+02   3.88e-02 2.40e+00
        pdb=" N   PRO A 500 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1132 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 655
        2.75 -     3.29: 6118
        3.29 -     3.82: 10709
        3.82 -     4.36: 12709
        4.36 -     4.90: 21987
  Nonbonded interactions: 52178
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER A 425 "
            pdb=" OD1 ASP A 427 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR A 229 "
            pdb=" OH  TYR A 516 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.277 3.040
  ... (remaining 52173 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=0.50 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:             0.430
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6450  Z= 0.134
  Angle     :  0.557   6.676   8771  Z= 0.315
  Chirality :  0.040   0.175    916
  Planarity :  0.004   0.077   1132
  Dihedral  : 15.107  89.992   2378
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.31), residues: 757
  helix:  2.02 (0.27), residues: 394
  sheet:  1.39 (0.85), residues: 39
  loop : -0.37 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 457 
 TYR   0.008   0.001   TYR A 381 
 PHE   0.021   0.001   PHE A 369 
 TRP   0.012   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6442)
  covalent geometry    : angle       0.55528 ( 8752)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       1.25207 (   10)
  hydrogen bonds       : bond        0.11812 (  317)
  hydrogen bonds       : angle       5.52982 (  907)
  link_NAG-ASN         : bond        0.00195 (    3)
  link_NAG-ASN         : angle       1.14455 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  483 GLU cc_start: 0.7026 (mp0) cc_final: 0.6688 (mp0)
REVERT: A  568 LEU cc_start: 0.7999 (tt) cc_final: 0.7580 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0889
  time to fit residues: 10.3523
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0870
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 580 ASN
B 498 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.164405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.136603 restraints weight = 10922.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.07
r_work: 0.3252 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6450  Z= 0.108
  Angle     :  0.486   5.974   8771  Z= 0.253
  Chirality :  0.040   0.159    916
  Planarity :  0.004   0.054   1132
  Dihedral  :  3.924  26.410    896
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.02 %
    Favored  : 95.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.31), residues: 757
  helix:  2.07 (0.26), residues: 392
  sheet:  1.10 (0.84), residues: 40
  loop : -0.26 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.025   0.001   TYR A 385 
 PHE   0.019   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6442)
  covalent geometry    : angle       0.48366 ( 8752)
  SS BOND              : bond        0.00462 (    5)
  SS BOND              : angle       1.10935 (   10)
  hydrogen bonds       : bond        0.04450 (  317)
  hydrogen bonds       : angle       4.52500 (  907)
  link_NAG-ASN         : bond        0.00250 (    3)
  link_NAG-ASN         : angle       1.20356 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   34 HIS cc_start: 0.8129 (m90) cc_final: 0.7916 (m90)
REVERT: A  492 PRO cc_start: 0.7743 (Cg_exo) cc_final: 0.7488 (Cg_endo)
REVERT: B  449 TYR cc_start: 0.7860 (m-80) cc_final: 0.7630 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0796
  time to fit residues: 9.2995
Evaluate side-chains
  78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 52 optimal weight:   30.0000
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.161481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.134842 restraints weight = 16362.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.11
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6450  Z= 0.123
  Angle     :  0.497   5.877   8771  Z= 0.260
  Chirality :  0.040   0.140    916
  Planarity :  0.004   0.043   1132
  Dihedral  :  3.831  20.655    896
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  4.76 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.31), residues: 757
  helix:  1.95 (0.26), residues: 398
  sheet:  0.48 (0.75), residues: 51
  loop : -0.19 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.026   0.001   TYR A 385 
 PHE   0.020   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6442)
  covalent geometry    : angle       0.49390 ( 8752)
  SS BOND              : bond        0.00426 (    5)
  SS BOND              : angle       1.13535 (   10)
  hydrogen bonds       : bond        0.04887 (  317)
  hydrogen bonds       : angle       4.47580 (  907)
  link_NAG-ASN         : bond        0.00216 (    3)
  link_NAG-ASN         : angle       1.49398 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  323 MET cc_start: 0.8016 (mmt) cc_final: 0.7538 (mmt)
REVERT: A  492 PRO cc_start: 0.7565 (Cg_exo) cc_final: 0.7276 (Cg_endo)
REVERT: B  420 ASP cc_start: 0.7727 (m-30) cc_final: 0.7417 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 78
  average time/residue: 0.0823
  time to fit residues: 8.3694
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0470
   chunk 50 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.7280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.162462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.136771 restraints weight = 11775.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.90
r_work: 0.3235 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6450  Z= 0.104
  Angle     :  0.471   5.839   8771  Z= 0.246
  Chirality :  0.039   0.125    916
  Planarity :  0.003   0.038   1132
  Dihedral  :  3.699  19.160    896
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.95 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.31), residues: 757
  helix:  2.05 (0.26), residues: 398
  sheet:  0.41 (0.75), residues: 51
  loop : -0.16 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.023   0.001   TYR A 385 
 PHE   0.018   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6442)
  covalent geometry    : angle       0.46856 ( 8752)
  SS BOND              : bond        0.00357 (    5)
  SS BOND              : angle       0.96396 (   10)
  hydrogen bonds       : bond        0.04369 (  317)
  hydrogen bonds       : angle       4.36036 (  907)
  link_NAG-ASN         : bond        0.00222 (    3)
  link_NAG-ASN         : angle       1.36963 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7694 (Cg_exo) cc_final: 0.7411 (Cg_endo)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.0776
  time to fit residues: 8.3230
Evaluate side-chains
  76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0170
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.0026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.162207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.135377 restraints weight = 14163.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.70
r_work: 0.3162 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6450  Z= 0.114
  Angle     :  0.481   5.865   8771  Z= 0.251
  Chirality :  0.040   0.125    916
  Planarity :  0.003   0.036   1132
  Dihedral  :  3.724  20.528    896
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.70 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.31), residues: 757
  helix:  1.99 (0.26), residues: 400
  sheet:  0.33 (0.75), residues: 51
  loop : -0.16 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 482 
 TYR   0.024   0.001   TYR A 385 
 PHE   0.018   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6442)
  covalent geometry    : angle       0.47776 ( 8752)
  SS BOND              : bond        0.00372 (    5)
  SS BOND              : angle       0.99988 (   10)
  hydrogen bonds       : bond        0.04625 (  317)
  hydrogen bonds       : angle       4.35703 (  907)
  link_NAG-ASN         : bond        0.00193 (    3)
  link_NAG-ASN         : angle       1.40986 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7647 (Cg_exo) cc_final: 0.7366 (Cg_endo)
REVERT: A  548 THR cc_start: 0.7974 (m) cc_final: 0.7379 (p)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.0811
  time to fit residues: 8.7309
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0670
   chunk 48 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    1.4922

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.132079 restraints weight = 18026.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.50
r_work: 0.3058 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6450  Z= 0.137
  Angle     :  0.512   5.910   8771  Z= 0.267
  Chirality :  0.041   0.134    916
  Planarity :  0.004   0.034   1132
  Dihedral  :  3.908  20.386    896
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.59 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.31), residues: 757
  helix:  1.89 (0.26), residues: 400
  sheet:  0.32 (0.75), residues: 51
  loop : -0.21 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 457 
 TYR   0.024   0.001   TYR A 385 
 PHE   0.019   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6442)
  covalent geometry    : angle       0.50882 ( 8752)
  SS BOND              : bond        0.00426 (    5)
  SS BOND              : angle       1.13397 (   10)
  hydrogen bonds       : bond        0.05176 (  317)
  hydrogen bonds       : angle       4.44572 (  907)
  link_NAG-ASN         : bond        0.00177 (    3)
  link_NAG-ASN         : angle       1.52913 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7723 (Cg_exo) cc_final: 0.7445 (Cg_endo)
  outliers start: 4
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0743
  time to fit residues: 7.8606
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0070
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.9404

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.153860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.127303 restraints weight = 12158.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.10
r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6450  Z= 0.160
  Angle     :  0.542   6.343   8771  Z= 0.283
  Chirality :  0.042   0.140    916
  Planarity :  0.004   0.033   1132
  Dihedral  :  4.112  21.946    896
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  6.99 %
    Favored  : 91.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.31), residues: 757
  helix:  1.69 (0.26), residues: 401
  sheet:  0.28 (0.75), residues: 51
  loop : -0.30 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 169 
 TYR   0.026   0.002   TYR A 385 
 PHE   0.018   0.002   PHE A 369 
 TRP   0.012   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6442)
  covalent geometry    : angle       0.53810 ( 8752)
  SS BOND              : bond        0.00499 (    5)
  SS BOND              : angle       1.30044 (   10)
  hydrogen bonds       : bond        0.05652 (  317)
  hydrogen bonds       : angle       4.55292 (  907)
  link_NAG-ASN         : bond        0.00184 (    3)
  link_NAG-ASN         : angle       1.66456 (    9)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.6903 (p0) cc_final: 0.6584 (p0)
REVERT: A  492 PRO cc_start: 0.7683 (Cg_exo) cc_final: 0.7404 (Cg_endo)
REVERT: B  449 TYR cc_start: 0.8267 (m-80) cc_final: 0.7946 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 83
  average time/residue: 0.0705
  time to fit residues: 7.9691
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3668 > 50:
  distance: 77 - 81:   8.679
  distance: 81 - 82:   6.602
  distance: 81 - 87:  31.906
  distance: 82 - 83:  20.173
  distance: 82 - 85:  12.344
  distance: 83 - 84:   9.602
  distance: 83 - 88:  32.130
  distance: 85 - 86:  27.724
  distance: 86 - 87:  11.626
  distance: 88 - 89:  17.537
  distance: 89 - 90:  31.907
  distance: 89 - 92:  40.905
  distance: 90 - 91:  22.369
  distance: 90 - 96:  28.272
  distance: 92 - 93:  27.807
  distance: 92 - 94:  34.501
  distance: 93 - 95:   7.583
  distance: 96 - 97:   4.006
  distance: 97 - 98:  20.524
  distance: 98 - 99:  33.419
  distance: 98 - 100:  30.696
  distance: 100 - 101:  13.192
  distance: 101 - 102:  13.185
  distance: 101 - 104:   8.164
  distance: 102 - 103:  21.452
  distance: 102 - 106:  55.281
  distance: 104 - 105:  29.568
  distance: 106 - 107:  43.266
  distance: 107 - 108:   9.442
  distance: 107 - 110:   9.126
  distance: 108 - 109:  32.187
  distance: 108 - 114:  20.241
  distance: 110 - 111:  18.927
  distance: 111 - 112:  27.158
  distance: 111 - 113:  47.936
  distance: 114 - 115:  12.039
  distance: 114 - 120:  12.018
  distance: 115 - 116:  23.675
  distance: 115 - 118:   8.495
  distance: 116 - 117:  16.008
  distance: 116 - 121:  52.529
  distance: 118 - 119:   8.230
  distance: 119 - 120:   6.636
  distance: 121 - 122:   7.043
  distance: 122 - 123:  12.168
  distance: 122 - 125:  41.060
  distance: 123 - 124:  10.316
  distance: 123 - 126:  26.903
  distance: 126 - 127:  13.546
  distance: 127 - 128:  10.347
  distance: 127 - 130:  17.287
  distance: 128 - 129:  21.908
  distance: 128 - 136:  18.671
  distance: 130 - 131:   9.343
  distance: 131 - 132:  15.574
  distance: 131 - 133:  21.524
  distance: 132 - 134:  29.287
  distance: 133 - 135:  20.870
  distance: 134 - 135:  16.730
  distance: 136 - 137:  26.811
  distance: 137 - 138:  21.782
  distance: 137 - 140:  18.405
  distance: 138 - 139:  11.846
  distance: 138 - 144:  44.251
  distance: 140 - 141:  18.596
  distance: 141 - 142:  40.997
  distance: 141 - 143:  28.166
  distance: 144 - 145:  21.107
  distance: 145 - 146:  18.721
  distance: 145 - 148:  10.833
  distance: 146 - 147:  20.218
  distance: 146 - 152:  14.315
  distance: 148 - 149:  44.418
  distance: 149 - 150:  24.717
  distance: 149 - 151:  10.105