Starting phenix.real_space_refine
on Wed Jul 23 08:56:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/07_2025/8dly_27520.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=  -0.002 sd=   0.032
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      13      5.16       5
     C    1582      2.51       5
     N     417      2.21       5
     O     471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2483
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1546
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 923
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 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: 2.73, per 1000 atoms: 1.10
  Number of scatterers: 2483
  At special positions: 0
  Unit cell: (68, 82, 69, 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      13     16.00
     O     471      8.00
     N     417      7.00
     C    1582      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " 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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 294.6 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  572

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 5 sheets defined
      13.4% alpha, 28.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.619A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 389
      removed outlier: 4.081A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.330A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.505A  pdb=" N   ASP H  89 " --> pdb=" O   ARG H  86 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 86 through 90'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.660A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.815A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.124A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   MET H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ASN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    186 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: 0.59

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 783
        1.34 -     1.46: 649
        1.46 -     1.58: 1102
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 2550
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.47e+00
  bond pdb=" CB  ASN H  50 "
       pdb=" CG  ASN H  50 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.38e+00
  bond pdb=" C   ALA C 520 "
       pdb=" N   PRO C 521 "
    ideal  model  delta    sigma   weight residual
    1.330  1.348 -0.018 1.19e-02 7.06e+03 2.32e+00
  bond pdb=" CB  GLU C 465 "
       pdb=" CG  GLU C 465 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.13e+00
  bond pdb=" CG  GLU C 465 "
       pdb=" CD  GLU C 465 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.71e+00
  ... (remaining 2545 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3270
        1.92 -     3.84: 172
        3.84 -     5.76: 21
        5.76 -     7.68: 4
        7.68 -     9.60: 2
  Bond angle restraints: 3469
  Sorted by residual:
  angle pdb=" CB  GLU C 465 "
        pdb=" CG  GLU C 465 "
        pdb=" CD  GLU C 465 "
      ideal   model   delta    sigma   weight residual
     112.60  118.87   -6.27 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" C   GLY C 476 "
        pdb=" N   SER C 477 "
        pdb=" CA  SER C 477 "
      ideal   model   delta    sigma   weight residual
     121.54  127.51   -5.97 1.91e+00 2.74e-01 9.78e+00
  angle pdb=" C   VAL C 483 "
        pdb=" N   GLU C 484 "
        pdb=" CA  GLU C 484 "
      ideal   model   delta    sigma   weight residual
     120.38  124.48   -4.10 1.37e+00 5.33e-01 8.95e+00
  angle pdb=" N   LEU C 518 "
        pdb=" CA  LEU C 518 "
        pdb=" C   LEU C 518 "
      ideal   model   delta    sigma   weight residual
     110.80  117.14   -6.34 2.13e+00 2.20e-01 8.87e+00
  angle pdb=" CA  LEU H  63 "
        pdb=" CB  LEU H  63 "
        pdb=" CG  LEU H  63 "
      ideal   model   delta    sigma   weight residual
     116.30  125.90   -9.60 3.50e+00 8.16e-02 7.52e+00
  ... (remaining 3464 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.75: 1306
       13.75 -    27.50: 146
       27.50 -    41.25: 38
       41.25 -    54.99: 9
       54.99 -    68.74: 1
  Dihedral angle restraints: 1500
    sinusoidal: 593
      harmonic: 907
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.09  -33.09     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CA  ASN C 487 "
           pdb=" C   ASN C 487 "
           pdb=" N   CYS C 488 "
           pdb=" CA  CYS C 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.29  -15.71     0      5.00e+00 4.00e-02 9.87e+00
  dihedral pdb=" CG  ARG C 509 "
           pdb=" CD  ARG C 509 "
           pdb=" NE  ARG C 509 "
           pdb=" CZ  ARG C 509 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.99   41.99     2      1.50e+01 4.44e-03 9.55e+00
  ... (remaining 1497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 224
       0.046 -    0.093: 100
       0.093 -    0.139: 38
       0.139 -    0.185: 5
       0.185 -    0.231: 3
  Chirality restraints: 370
  Sorted by residual:
  chirality pdb=" CB  THR C 470 "
            pdb=" CA  THR C 470 "
            pdb=" OG1 THR C 470 "
            pdb=" CG2 THR C 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  MET H 106 "
            pdb=" N   MET H 106 "
            pdb=" C   MET H 106 "
            pdb=" CB  MET H 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 367 not shown)

  Planarity restraints: 449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 520 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" C   ALA C 520 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA C 520 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO C 521 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN H  60 "    0.035 5.00e-02 4.00e+02   5.30e-02 4.49e+00
        pdb=" N   PRO H  61 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO H  61 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H  61 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H  40 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO H  41 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "    0.025 5.00e-02 4.00e+02
  ... (remaining 446 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 789
        2.83 -     3.35: 1927
        3.35 -     3.87: 4036
        3.87 -     4.38: 4493
        4.38 -     4.90: 8057
  Nonbonded interactions: 19302
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 450 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" NE  ARG C 457 "
            pdb=" OD2 ASP C 467 "
     model   vdw
     2.432 3.120
  nonbonded pdb=" O   ILE C 418 "
            pdb=" N   TYR C 423 "
     model   vdw
     2.487 3.120
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" O4  NAG C1301 "
            pdb=" O6  NAG C1301 "
     model   vdw
     2.524 3.040
  ... (remaining 19297 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:             2.590
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.960
  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:15.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
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      :  0.005   0.051   2556  Z= 0.237
  Angle     :  0.945   9.601   3482  Z= 0.513
  Chirality :  0.059   0.231    370
  Planarity :  0.006   0.053    448
  Dihedral  : 12.405  68.742    913
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.00 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.40), residues: 310
  helix: -3.94 (0.60), residues: 26
  sheet: -0.08 (0.45), residues: 104
  loop : -1.03 (0.37), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP H  47 
 HIS   0.011   0.003   HIS H  35 
 PHE   0.017   0.002   PHE H  27 
 TYR   0.015   0.002   TYR C 453 
 ARG   0.007   0.001   ARG H  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    1)
  link_NAG-ASN         : angle       3.46937 (    3)
  hydrogen bonds       : bond        0.13741 (   74)
  hydrogen bonds       : angle       9.45269 (  186)
  SS BOND              : bond        0.00516 (    5)
  SS BOND              : angle       1.21448 (   10)
  covalent geometry    : bond        0.00521 ( 2550)
  covalent geometry    : angle       0.93943 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C  420 ASP cc_start: 0.8522 (m-30) cc_final: 0.8206 (m-30)
REVERT: C  424 LYS cc_start: 0.8840 (tptt) cc_final: 0.8594 (tppp)
REVERT: C  456 PHE cc_start: 0.8663 (t80) cc_final: 0.8216 (t80)
REVERT: C  474 GLN cc_start: 0.7637 (mt0) cc_final: 0.7419 (mt0)
REVERT: H   39 GLN cc_start: 0.7728 (pt0) cc_final: 0.7151 (pm20)
REVERT: H   86 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6622 (mtp180)
REVERT: H   92 ILE cc_start: 0.8541 (mt) cc_final: 0.7759 (mm)
  outliers start: 1
  outliers final: 2
  residues processed: 100
  average time/residue: 1.1699
  time to fit residues: 119.6071
Evaluate side-chains
  63 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0770
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
C 474 GLN
C 506 GLN
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.088945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.076829 restraints weight = 5947.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 3.17
r_work: 0.3109 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2556  Z= 0.127
  Angle     :  0.599   6.518   3482  Z= 0.296
  Chirality :  0.044   0.140    370
  Planarity :  0.004   0.032    448
  Dihedral  :  8.726 124.730    377
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 16.85 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.42), residues: 310
  helix: -3.58 (0.75), residues: 26
  sheet:  0.11 (0.48), residues: 98
  loop : -0.56 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.006   0.001   PHE H  29 
 TYR   0.014   0.001   TYR H  79 
 ARG   0.005   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    1)
  link_NAG-ASN         : angle       1.98271 (    3)
  hydrogen bonds       : bond        0.03250 (   74)
  hydrogen bonds       : angle       7.29564 (  186)
  SS BOND              : bond        0.00201 (    5)
  SS BOND              : angle       0.71615 (   10)
  covalent geometry    : bond        0.00295 ( 2550)
  covalent geometry    : angle       0.59586 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.8386 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8734 (m-30) cc_final: 0.8478 (m-30)
REVERT: C  424 LYS cc_start: 0.8985 (tptt) cc_final: 0.8712 (tppp)
REVERT: C  456 PHE cc_start: 0.8895 (t80) cc_final: 0.8406 (t80)
REVERT: H   29 PHE cc_start: 0.8492 (t80) cc_final: 0.8201 (t80)
REVERT: H   60 ASN cc_start: 0.9028 (t0) cc_final: 0.8799 (t0)
REVERT: H   86 ARG cc_start: 0.7330 (mtp180) cc_final: 0.6586 (mtp180)
  outliers start: 10
  outliers final: 6
  residues processed: 78
  average time/residue: 1.2060
  time to fit residues: 96.0674
Evaluate side-chains
  69 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   27 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0980
   chunk 22 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.087411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.075067 restraints weight = 5841.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.24
r_work: 0.3091 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2556  Z= 0.153
  Angle     :  0.590   6.381   3482  Z= 0.296
  Chirality :  0.044   0.134    370
  Planarity :  0.004   0.033    448
  Dihedral  :  5.307  44.479    375
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 18.35 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.43), residues: 310
  helix: -3.48 (1.03), residues: 20
  sheet:  0.12 (0.47), residues: 103
  loop : -0.76 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.007   0.001   PHE C 347 
 TYR   0.010   0.001   TYR C 495 
 ARG   0.007   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00342 (    1)
  link_NAG-ASN         : angle       2.11197 (    3)
  hydrogen bonds       : bond        0.02960 (   74)
  hydrogen bonds       : angle       6.93129 (  186)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.59011 (   10)
  covalent geometry    : bond        0.00349 ( 2550)
  covalent geometry    : angle       0.58740 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8669 (m-30) cc_final: 0.8394 (m-30)
REVERT: C  424 LYS cc_start: 0.9001 (tptt) cc_final: 0.8729 (tppp)
REVERT: C  444 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8109 (mtmm)
REVERT: H   60 ASN cc_start: 0.8991 (t0) cc_final: 0.8769 (t0)
REVERT: H   86 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6649 (mtp180)
REVERT: H   88 GLU cc_start: 0.9003 (pp20) cc_final: 0.8730 (pp20)
REVERT: H   89 ASP cc_start: 0.8043 (m-30) cc_final: 0.7776 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 74
  average time/residue: 1.1570
  time to fit residues: 87.5441
Evaluate side-chains
  68 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0770
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.088081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.075795 restraints weight = 5923.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.17
r_work: 0.3086 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2556  Z= 0.133
  Angle     :  0.571   6.991   3482  Z= 0.283
  Chirality :  0.043   0.134    370
  Planarity :  0.004   0.034    448
  Dihedral  :  5.061  42.759    373
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.22 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.43), residues: 310
  helix: -3.28 (1.11), residues: 20
  sheet:  0.05 (0.47), residues: 105
  loop : -0.71 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.006   0.001   PHE C 347 
 TYR   0.009   0.001   TYR C 495 
 ARG   0.010   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00297 (    1)
  link_NAG-ASN         : angle       1.92534 (    3)
  hydrogen bonds       : bond        0.02743 (   74)
  hydrogen bonds       : angle       6.78079 (  186)
  SS BOND              : bond        0.00174 (    5)
  SS BOND              : angle       0.41168 (   10)
  covalent geometry    : bond        0.00310 ( 2550)
  covalent geometry    : angle       0.56908 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8641 (m-30) cc_final: 0.8370 (m-30)
REVERT: C  424 LYS cc_start: 0.8995 (tptt) cc_final: 0.8722 (tppp)
REVERT: C  444 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8099 (mtmm)
REVERT: H   29 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7218 (t80)
REVERT: H   37 VAL cc_start: 0.9269 (t) cc_final: 0.9067 (m)
REVERT: H   60 ASN cc_start: 0.8990 (t0) cc_final: 0.8787 (t0)
REVERT: H   74 SER cc_start: 0.9192 (m) cc_final: 0.8919 (t)
REVERT: H   86 ARG cc_start: 0.7304 (mtp180) cc_final: 0.6569 (mtp180)
REVERT: H   88 GLU cc_start: 0.9035 (pp20) cc_final: 0.8668 (pp20)
REVERT: H   89 ASP cc_start: 0.8088 (m-30) cc_final: 0.7819 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 73
  average time/residue: 1.2363
  time to fit residues: 92.3047
Evaluate side-chains
  72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 474 GLN
C 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.086444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.073963 restraints weight = 5962.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.28
r_work: 0.3061 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2556  Z= 0.161
  Angle     :  0.593   7.620   3482  Z= 0.293
  Chirality :  0.044   0.133    370
  Planarity :  0.004   0.033    448
  Dihedral  :  5.077  44.485    373
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 21.35 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.44), residues: 310
  helix: -3.11 (1.18), residues: 20
  sheet: -0.03 (0.46), residues: 110
  loop : -0.62 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.007   0.001   PHE C 347 
 TYR   0.010   0.001   TYR C 495 
 ARG   0.009   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    1)
  link_NAG-ASN         : angle       1.96801 (    3)
  hydrogen bonds       : bond        0.02801 (   74)
  hydrogen bonds       : angle       6.65230 (  186)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.37343 (   10)
  covalent geometry    : bond        0.00371 ( 2550)
  covalent geometry    : angle       0.59107 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8664 (ttm-80)
REVERT: C  420 ASP cc_start: 0.8617 (m-30) cc_final: 0.8329 (m-30)
REVERT: C  424 LYS cc_start: 0.8981 (tptt) cc_final: 0.8633 (tppp)
REVERT: C  444 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8124 (mtmm)
REVERT: H   39 GLN cc_start: 0.8026 (pt0) cc_final: 0.7653 (tt0)
REVERT: H   60 ASN cc_start: 0.9005 (t0) cc_final: 0.8804 (t0)
REVERT: H   74 SER cc_start: 0.9202 (m) cc_final: 0.8930 (t)
REVERT: H   86 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6586 (mtp180)
REVERT: H   88 GLU cc_start: 0.9053 (pp20) cc_final: 0.8616 (pp20)
  outliers start: 15
  outliers final: 8
  residues processed: 74
  average time/residue: 1.2059
  time to fit residues: 91.3175
Evaluate side-chains
  75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0030
   overall best weight:    1.0794

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.085212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072733 restraints weight = 5977.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.26
r_work: 0.3031 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   2556  Z= 0.197
  Angle     :  0.610   6.856   3482  Z= 0.306
  Chirality :  0.045   0.135    370
  Planarity :  0.004   0.028    448
  Dihedral  :  5.281  45.992    373
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 22.10 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.45), residues: 310
  helix: -2.96 (1.00), residues: 26
  sheet: -0.20 (0.46), residues: 110
  loop : -0.74 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.007   0.001   PHE C 347 
 TYR   0.013   0.001   TYR H 101 
 ARG   0.007   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00198 (    1)
  link_NAG-ASN         : angle       2.05971 (    3)
  hydrogen bonds       : bond        0.03065 (   74)
  hydrogen bonds       : angle       6.65984 (  186)
  SS BOND              : bond        0.00275 (    5)
  SS BOND              : angle       0.41216 (   10)
  covalent geometry    : bond        0.00454 ( 2550)
  covalent geometry    : angle       0.60752 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8610 (m-30) cc_final: 0.8380 (m-30)
REVERT: C  424 LYS cc_start: 0.8998 (tptt) cc_final: 0.8677 (tppp)
REVERT: C  444 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8144 (mtmm)
REVERT: C  516 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6567 (tm-30)
REVERT: H   39 GLN cc_start: 0.8100 (pt0) cc_final: 0.7732 (tt0)
REVERT: H   74 SER cc_start: 0.9221 (m) cc_final: 0.8967 (t)
REVERT: H   86 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6651 (mtp180)
REVERT: H   88 GLU cc_start: 0.9049 (pp20) cc_final: 0.8604 (pp20)
REVERT: H   89 ASP cc_start: 0.8137 (m-30) cc_final: 0.7840 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 73
  average time/residue: 1.1347
  time to fit residues: 84.7341
Evaluate side-chains
  72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   54 ASP
Chi-restraints excluded: chain H residue  113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3394 r_free = 0.3394 target = 0.085366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072683 restraints weight = 6056.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 3.29
r_work: 0.3032 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2556  Z= 0.187
  Angle     :  0.652   8.544   3482  Z= 0.318
  Chirality :  0.045   0.142    370
  Planarity :  0.004   0.036    448
  Dihedral  :  5.326  46.167    373
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.97 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.45), residues: 310
  helix: -2.92 (0.98), residues: 26
  sheet: -0.23 (0.47), residues: 107
  loop : -0.68 (0.43), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.007   0.001   PHE C 347 
 TYR   0.010   0.001   TYR C 495 
 ARG   0.009   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       2.04709 (    3)
  hydrogen bonds       : bond        0.03186 (   74)
  hydrogen bonds       : angle       6.63946 (  186)
  SS BOND              : bond        0.00253 (    5)
  SS BOND              : angle       0.81444 (   10)
  covalent geometry    : bond        0.00437 ( 2550)
  covalent geometry    : angle       0.64889 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8708 (ptm-80) cc_final: 0.8499 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8592 (m-30) cc_final: 0.8372 (m-30)
REVERT: C  424 LYS cc_start: 0.8974 (tptt) cc_final: 0.8645 (tppp)
REVERT: C  444 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8112 (mtmm)
REVERT: C  516 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6900 (tm-30)
REVERT: H   39 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7707 (tt0)
REVERT: H   74 SER cc_start: 0.9227 (m) cc_final: 0.8970 (t)
REVERT: H   86 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6633 (mtp180)
REVERT: H   88 GLU cc_start: 0.9067 (pp20) cc_final: 0.8609 (pp20)
REVERT: H   89 ASP cc_start: 0.8173 (m-30) cc_final: 0.7848 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 72
  average time/residue: 1.1917
  time to fit residues: 87.7582
Evaluate side-chains
  72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 20 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.086869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.074309 restraints weight = 5938.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.25
r_work: 0.3063 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2556  Z= 0.124
  Angle     :  0.607   8.116   3482  Z= 0.298
  Chirality :  0.043   0.135    370
  Planarity :  0.004   0.039    448
  Dihedral  :  4.887  41.174    373
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 24.34 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.44), residues: 310
  helix: -2.88 (1.17), residues: 20
  sheet: -0.10 (0.51), residues: 92
  loop : -0.64 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.005   0.001   PHE C 515 
 TYR   0.012   0.001   TYR H 101 
 ARG   0.009   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       1.84463 (    3)
  hydrogen bonds       : bond        0.02765 (   74)
  hydrogen bonds       : angle       6.44520 (  186)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.64821 (   10)
  covalent geometry    : bond        0.00295 ( 2550)
  covalent geometry    : angle       0.60472 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8462 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8998 (tptt) cc_final: 0.8672 (tppp)
REVERT: C  444 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8141 (mtmm)
REVERT: C  516 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6988 (tm-30)
REVERT: H   39 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7659 (tt0)
REVERT: H   74 SER cc_start: 0.9198 (m) cc_final: 0.8966 (t)
REVERT: H   86 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6565 (mtp180)
REVERT: H   88 GLU cc_start: 0.9097 (pp20) cc_final: 0.8683 (pp20)
REVERT: H   89 ASP cc_start: 0.8100 (m-30) cc_final: 0.7884 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 75
  average time/residue: 1.2349
  time to fit residues: 94.5556
Evaluate side-chains
  75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   39 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0030
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.087354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.074816 restraints weight = 5916.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.26
r_work: 0.3077 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2556  Z= 0.132
  Angle     :  0.632   7.743   3482  Z= 0.313
  Chirality :  0.044   0.144    370
  Planarity :  0.004   0.040    448
  Dihedral  :  4.777  39.149    373
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.09 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.45), residues: 310
  helix: -2.79 (1.20), residues: 20
  sheet: -0.07 (0.48), residues: 100
  loop : -0.59 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.009   0.001   PHE H  29 
 TYR   0.008   0.001   TYR C 495 
 ARG   0.009   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       1.75976 (    3)
  hydrogen bonds       : bond        0.02924 (   74)
  hydrogen bonds       : angle       6.38213 (  186)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       0.48060 (   10)
  covalent geometry    : bond        0.00317 ( 2550)
  covalent geometry    : angle       0.63025 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8466 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8999 (tptt) cc_final: 0.8642 (tppp)
REVERT: C  444 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8143 (mtmm)
REVERT: C  516 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6798 (tm-30)
REVERT: C  517 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7693 (tm)
REVERT: H   39 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7612 (tt0)
REVERT: H   74 SER cc_start: 0.9141 (m) cc_final: 0.8932 (t)
REVERT: H   86 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6635 (mtp180)
REVERT: H   88 GLU cc_start: 0.9094 (pp20) cc_final: 0.8669 (pp20)
REVERT: H   89 ASP cc_start: 0.8110 (m-30) cc_final: 0.7897 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 73
  average time/residue: 1.1752
  time to fit residues: 87.6737
Evaluate side-chains
  71 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   39 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0070
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.086381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.073960 restraints weight = 5942.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.22
r_work: 0.3062 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2556  Z= 0.151
  Angle     :  0.640   8.061   3482  Z= 0.316
  Chirality :  0.044   0.136    370
  Planarity :  0.005   0.042    448
  Dihedral  :  4.792  40.611    373
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.22 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.45), residues: 310
  helix: -2.71 (1.23), residues: 20
  sheet: -0.19 (0.48), residues: 102
  loop : -0.56 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.006   0.001   PHE C 347 
 TYR   0.014   0.001   TYR H 101 
 ARG   0.009   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    1)
  link_NAG-ASN         : angle       1.84098 (    3)
  hydrogen bonds       : bond        0.02831 (   74)
  hydrogen bonds       : angle       6.42746 (  186)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.49709 (   10)
  covalent geometry    : bond        0.00355 ( 2550)
  covalent geometry    : angle       0.63790 ( 3469)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8711 (ptm-80) cc_final: 0.8471 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8501 (m-30) cc_final: 0.8150 (m-30)
REVERT: C  424 LYS cc_start: 0.8992 (tptt) cc_final: 0.8623 (tppp)
REVERT: C  444 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8149 (mtmm)
REVERT: C  516 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6789 (tm-30)
REVERT: H   39 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: H   74 SER cc_start: 0.9140 (m) cc_final: 0.8933 (t)
REVERT: H   86 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6599 (mtp180)
REVERT: H   88 GLU cc_start: 0.9066 (pp20) cc_final: 0.8625 (pp20)
REVERT: H   89 ASP cc_start: 0.8176 (m-30) cc_final: 0.7942 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 67
  average time/residue: 1.2171
  time to fit residues: 83.3746
Evaluate side-chains
  71 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   39 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    0.0670
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0040
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4930

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.087440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.074867 restraints weight = 5982.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.26
r_work: 0.3079 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2556  Z= 0.132
  Angle     :  0.645   8.657   3482  Z= 0.318
  Chirality :  0.044   0.136    370
  Planarity :  0.005   0.038    448
  Dihedral  :  4.717  39.311    373
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.22 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.45), residues: 310
  helix: -2.74 (1.21), residues: 20
  sheet: -0.06 (0.50), residues: 93
  loop : -0.63 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.014   0.001   PHE H  29 
 TYR   0.010   0.001   TYR H  32 
 ARG   0.009   0.001   ARG H  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       1.78308 (    3)
  hydrogen bonds       : bond        0.03018 (   74)
  hydrogen bonds       : angle       6.45663 (  186)
  SS BOND              : bond        0.00159 (    5)
  SS BOND              : angle       0.51133 (   10)
  covalent geometry    : bond        0.00315 ( 2550)
  covalent geometry    : angle       0.64325 ( 3469)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2721.03 seconds
wall clock time: 47 minutes 9.96 seconds (2829.96 seconds total)