Starting phenix.real_space_refine
on Fri Aug 22 14:03:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bfj_44498/08_2025/9bfj_44498.map"
  }
  resolution = 2.35
  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=   0.002 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    2564      2.51       5
     N     578      2.21       5
     O     669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 3833
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 3824
          Classifications: {'peptide': 496}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Unusual residues: {' CL': 1, ' NA': 1, 'CHT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.11, per 1000 atoms: 0.29
  Number of scatterers: 3833
  At special positions: 0
  Unit cell: (73.062, 82.656, 74.538, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     Na      1     11.00
     O     669      8.00
     N     578      7.00
     C    2564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 100.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  904

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      78.4% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 29
      removed outlier: 3.805A  pdb=" N   LEU A   8 " --> pdb=" O   HIS A   4 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A  21 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY A  22 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 63
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 81 through 84
    Processing helix  chain 'A' and resid 85 through 102
      removed outlier: 4.701A  pdb=" N   ILE A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU A  95 " --> pdb=" O   TYR A  91 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE A  96 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 123 through 157
      removed outlier: 3.701A  pdb=" N   ILE A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      Proline residue:  A 133  - end of helix
    Processing helix  chain 'A' and resid 160 through 182
      removed outlier: 3.582A  pdb=" N   TYR A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 208
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 4.043A  pdb=" N   VAL A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 250
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 4.027A  pdb=" N   ARG A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 297
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 318 through 327
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 4.010A  pdb=" N   SER A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 399
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.981A  pdb=" N   LEU A 405 " --> pdb=" O   THR A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 426
      removed outlier: 4.327A  pdb=" N   PHE A 418 " --> pdb=" O   TYR A 414 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 449
    Processing helix  chain 'A' and resid 478 through 505
    Processing helix  chain 'A' and resid 508 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467

    277 hydrogen bonds defined for protein.
    819 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: 0.49

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1110
        1.34 -     1.46: 920
        1.46 -     1.58: 1875
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 3940
  Sorted by residual:
  bond pdb=" C5  CHT A 801 "
       pdb=" N1  CHT A 801 "
    ideal  model  delta    sigma   weight residual
    1.509  1.455  0.054 2.00e-02 2.50e+03 7.33e+00
  bond pdb=" C8  CHT A 801 "
       pdb=" N1  CHT A 801 "
    ideal  model  delta    sigma   weight residual
    1.492  1.440  0.052 2.00e-02 2.50e+03 6.82e+00
  bond pdb=" C7  CHT A 801 "
       pdb=" N1  CHT A 801 "
    ideal  model  delta    sigma   weight residual
    1.492  1.458  0.034 2.00e-02 2.50e+03 2.92e+00
  bond pdb=" C6  CHT A 801 "
       pdb=" N1  CHT A 801 "
    ideal  model  delta    sigma   weight residual
    1.487  1.460  0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" C   ILE A 252 "
       pdb=" N   PRO A 253 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.37e+00
  ... (remaining 3935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 5258
        1.77 -     3.54: 100
        3.54 -     5.30: 12
        5.30 -     7.07: 10
        7.07 -     8.84: 2
  Bond angle restraints: 5382
  Sorted by residual:
  angle pdb=" CA  LEU A 273 "
        pdb=" CB  LEU A 273 "
        pdb=" CG  LEU A 273 "
      ideal   model   delta    sigma   weight residual
     116.30  125.14   -8.84 3.50e+00 8.16e-02 6.38e+00
  angle pdb=" CA  ILE A 383 "
        pdb=" CB  ILE A 383 "
        pdb=" CG1 ILE A 383 "
      ideal   model   delta    sigma   weight residual
     110.40  114.60   -4.20 1.70e+00 3.46e-01 6.11e+00
  angle pdb=" OG1 THR A 313 "
        pdb=" CB  THR A 313 "
        pdb=" CG2 THR A 313 "
      ideal   model   delta    sigma   weight residual
     109.30  104.91    4.39 2.00e+00 2.50e-01 4.82e+00
  angle pdb=" C   ASP A 309 "
        pdb=" CA  ASP A 309 "
        pdb=" CB  ASP A 309 "
      ideal   model   delta    sigma   weight residual
     109.51  113.53   -4.02 1.85e+00 2.92e-01 4.73e+00
  angle pdb=" C   ILE A 252 "
        pdb=" N   PRO A 253 "
        pdb=" CD  PRO A 253 "
      ideal   model   delta    sigma   weight residual
     125.00  133.23   -8.23 4.10e+00 5.95e-02 4.03e+00
  ... (remaining 5377 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 1985
       17.11 -    34.21: 190
       34.21 -    51.32: 42
       51.32 -    68.42: 9
       68.42 -    85.53: 6
  Dihedral angle restraints: 2232
    sinusoidal: 804
      harmonic: 1428
  Sorted by residual:
  dihedral pdb=" CG  LYS A 226 "
           pdb=" CD  LYS A 226 "
           pdb=" CE  LYS A 226 "
           pdb=" NZ  LYS A 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.13   57.13     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   LEU A  51 "
           pdb=" CA  LEU A  51 "
           pdb=" CB  LEU A  51 "
           pdb=" CG  LEU A  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.52   54.52     3      1.50e+01 4.44e-03 9.29e+00
  dihedral pdb=" CA  MET A 395 "
           pdb=" CB  MET A 395 "
           pdb=" CG  MET A 395 "
           pdb=" SD  MET A 395 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.17   53.83     3      1.50e+01 4.44e-03 9.24e+00
  ... (remaining 2229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 330
       0.028 -    0.057: 189
       0.057 -    0.085: 69
       0.085 -    0.113: 23
       0.113 -    0.141: 13
  Chirality restraints: 624
  Sorted by residual:
  chirality pdb=" CB  VAL A 424 "
            pdb=" CA  VAL A 424 "
            pdb=" CG1 VAL A 424 "
            pdb=" CG2 VAL A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CB  VAL A 380 "
            pdb=" CA  VAL A 380 "
            pdb=" CG1 VAL A 380 "
            pdb=" CG2 VAL A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  PRO A 310 "
            pdb=" N   PRO A 310 "
            pdb=" C   PRO A 310 "
            pdb=" CB  PRO A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 621 not shown)

  Planarity restraints: 651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 242 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   ASP A 242 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ASP A 242 "    0.014 2.00e-02 2.50e+03
        pdb=" N   SER A 243 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  67 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.69e+00
        pdb=" C   TYR A  67 "    0.037 2.00e-02 2.50e+03
        pdb=" O   TYR A  67 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A  68 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 240 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" C   TRP A 240 "    0.031 2.00e-02 2.50e+03
        pdb=" O   TRP A 240 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 241 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 648 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 238
        2.74 -     3.28: 3920
        3.28 -     3.82: 6814
        3.82 -     4.36: 7880
        4.36 -     4.90: 13608
  Nonbonded interactions: 32460
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  63 "
            pdb="NA    NA A 803 "
     model   vdw
     2.196 2.470
  nonbonded pdb=" O   GLY A 389 "
            pdb=" OG1 THR A 393 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ALA A  60 "
            pdb="NA    NA A 803 "
     model   vdw
     2.226 2.470
  nonbonded pdb=" O   ALA A 169 "
            pdb=" OG1 THR A 173 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ASN A 491 "
            pdb=" OG  SER A 495 "
     model   vdw
     2.262 3.040
  ... (remaining 32455 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.160
  Find NCS groups from input model:        0.030
  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:7.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
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   0.054   3940  Z= 0.203
  Angle     :  0.654   8.840   5382  Z= 0.342
  Chirality :  0.043   0.141    624
  Planarity :  0.006   0.037    651
  Dihedral  : 15.095  85.531   1328
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.47 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.78 (0.36), residues: 490
  helix:  0.87 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.38 (0.56), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 260 
 TYR   0.020   0.002   TYR A 269 
 PHE   0.013   0.002   PHE A   3 
 TRP   0.008   0.002   TRP A 379 
 HIS   0.002   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3940)
  covalent geometry    : angle       0.65352 ( 5382)
  hydrogen bonds       : bond        0.13012 (  277)
  hydrogen bonds       : angle       5.83275 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  382 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6784 (mtm-85)
REVERT: A  386 PHE cc_start: 0.7753 (m-80) cc_final: 0.6674 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.4730
  time to fit residues: 24.0728
Evaluate side-chains
  46 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.152207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.105544 restraints weight = 4045.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.10
r_work: 0.3048 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3940  Z= 0.111
  Angle     :  0.474   6.616   5382  Z= 0.246
  Chirality :  0.036   0.123    624
  Planarity :  0.004   0.033    651
  Dihedral  :  4.495  57.434    535
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.97 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.90 (0.38), residues: 490
  helix:  1.70 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -0.12 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 446 
 TYR   0.012   0.001   TYR A 269 
 PHE   0.007   0.001   PHE A 244 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.002   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3940)
  covalent geometry    : angle       0.47374 ( 5382)
  hydrogen bonds       : bond        0.04223 (  277)
  hydrogen bonds       : angle       4.41144 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  386 PHE cc_start: 0.7792 (m-80) cc_final: 0.6551 (t80)
REVERT: A  400 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7966 (tptp)
  outliers start: 6
  outliers final: 0
  residues processed: 50
  average time/residue: 0.4118
  time to fit residues: 21.5393
Evaluate side-chains
  49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 44 optimal weight:    0.0070
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.152868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.106510 restraints weight = 4084.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.27
r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3940  Z= 0.110
  Angle     :  0.477  10.457   5382  Z= 0.240
  Chirality :  0.036   0.123    624
  Planarity :  0.004   0.030    651
  Dihedral  :  4.461  58.822    535
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.47 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.04 (0.38), residues: 490
  helix:  1.82 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.21 (0.57), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.010   0.001   TYR A 182 
 PHE   0.006   0.001   PHE A 244 
 TRP   0.006   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 3940)
  covalent geometry    : angle       0.47653 ( 5382)
  hydrogen bonds       : bond        0.04001 (  277)
  hydrogen bonds       : angle       4.24571 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  386 PHE cc_start: 0.7841 (m-80) cc_final: 0.6629 (t80)
REVERT: A  400 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7945 (tptp)
  outliers start: 6
  outliers final: 1
  residues processed: 55
  average time/residue: 0.3777
  time to fit residues: 21.8199
Evaluate side-chains
  52 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0670
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.1722

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.150813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103587 restraints weight = 4035.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.15
r_work: 0.3059 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3940  Z= 0.135
  Angle     :  0.498   7.623   5382  Z= 0.254
  Chirality :  0.038   0.129    624
  Planarity :  0.004   0.029    651
  Dihedral  :  4.385  51.065    535
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.22 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  1.93 (0.38), residues: 490
  helix:  1.74 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.22 (0.58), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.010   0.001   TYR A 331 
 PHE   0.009   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3940)
  covalent geometry    : angle       0.49790 ( 5382)
  hydrogen bonds       : bond        0.04390 (  277)
  hydrogen bonds       : angle       4.35819 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  386 PHE cc_start: 0.7880 (m-80) cc_final: 0.6635 (t80)
REVERT: A  400 LYS cc_start: 0.8590 (mmtm) cc_final: 0.7956 (tptp)
  outliers start: 6
  outliers final: 1
  residues processed: 50
  average time/residue: 0.4306
  time to fit residues: 22.5612
Evaluate side-chains
  49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108550 restraints weight = 4086.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.96
r_work: 0.3093 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3940  Z= 0.105
  Angle     :  0.457   6.436   5382  Z= 0.233
  Chirality :  0.036   0.125    624
  Planarity :  0.003   0.028    651
  Dihedral  :  4.110  45.738    535
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.47 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.02 (0.38), residues: 490
  helix:  1.80 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.30 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 446 
 TYR   0.008   0.001   TYR A 269 
 PHE   0.007   0.001   PHE A 196 
 TRP   0.008   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 3940)
  covalent geometry    : angle       0.45744 ( 5382)
  hydrogen bonds       : bond        0.03798 (  277)
  hydrogen bonds       : angle       4.18148 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  386 PHE cc_start: 0.7821 (m-80) cc_final: 0.6595 (t80)
REVERT: A  400 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7865 (tptp)
  outliers start: 7
  outliers final: 3
  residues processed: 54
  average time/residue: 0.4337
  time to fit residues: 24.5325
Evaluate side-chains
  53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.105077 restraints weight = 4134.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.18
r_work: 0.3081 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   3940  Z= 0.113
  Angle     :  0.464   6.063   5382  Z= 0.238
  Chirality :  0.037   0.125    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.115  44.904    535
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.72 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.01 (0.38), residues: 490
  helix:  1.78 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.26 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.009   0.001   TYR A 331 
 PHE   0.006   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3940)
  covalent geometry    : angle       0.46408 ( 5382)
  hydrogen bonds       : bond        0.03941 (  277)
  hydrogen bonds       : angle       4.21329 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7374 (tt)
REVERT: A  386 PHE cc_start: 0.7854 (m-80) cc_final: 0.6618 (t80)
REVERT: A  400 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7888 (tptp)
  outliers start: 8
  outliers final: 4
  residues processed: 55
  average time/residue: 0.3543
  time to fit residues: 20.5342
Evaluate side-chains
  55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 6 optimal weight:    0.1980
   chunk 32 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.153512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.106507 restraints weight = 4155.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.14
r_work: 0.3096 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   3940  Z= 0.107
  Angle     :  0.460   6.101   5382  Z= 0.237
  Chirality :  0.036   0.123    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.060  44.479    535
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.47 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.08 (0.38), residues: 490
  helix:  1.83 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.24 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 446 
 TYR   0.009   0.001   TYR A 269 
 PHE   0.007   0.001   PHE A 196 
 TRP   0.008   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3940)
  covalent geometry    : angle       0.46041 ( 5382)
  hydrogen bonds       : bond        0.03772 (  277)
  hydrogen bonds       : angle       4.14201 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7416 (tt)
REVERT: A  386 PHE cc_start: 0.7849 (m-80) cc_final: 0.6624 (t80)
REVERT: A  400 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7882 (tptp)
  outliers start: 9
  outliers final: 4
  residues processed: 58
  average time/residue: 0.3840
  time to fit residues: 23.3949
Evaluate side-chains
  59 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 48 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.153017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105696 restraints weight = 4151.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.19
r_work: 0.3088 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   3940  Z= 0.111
  Angle     :  0.467   6.082   5382  Z= 0.241
  Chirality :  0.037   0.123    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.073  44.125    535
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.72 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.06 (0.38), residues: 490
  helix:  1.82 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.26 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 382 
 TYR   0.009   0.001   TYR A 175 
 PHE   0.006   0.001   PHE A 196 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3940)
  covalent geometry    : angle       0.46713 ( 5382)
  hydrogen bonds       : bond        0.03854 (  277)
  hydrogen bonds       : angle       4.15914 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7403 (tt)
REVERT: A  386 PHE cc_start: 0.7836 (m-80) cc_final: 0.6591 (t80)
REVERT: A  400 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7825 (tptp)
  outliers start: 10
  outliers final: 5
  residues processed: 59
  average time/residue: 0.3892
  time to fit residues: 24.0790
Evaluate side-chains
  58 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 36 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:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.152654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105448 restraints weight = 4110.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.17
r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3940  Z= 0.117
  Angle     :  0.490  10.108   5382  Z= 0.248
  Chirality :  0.037   0.123    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.106  43.507    535
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.47 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.03 (0.38), residues: 490
  helix:  1.80 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.25 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 369 
 TYR   0.009   0.001   TYR A 175 
 PHE   0.006   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3940)
  covalent geometry    : angle       0.49024 ( 5382)
  hydrogen bonds       : bond        0.03961 (  277)
  hydrogen bonds       : angle       4.19238 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7454 (tt)
REVERT: A  386 PHE cc_start: 0.7860 (m-80) cc_final: 0.6624 (t80)
REVERT: A  400 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7858 (tptp)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.3962
  time to fit residues: 23.6885
Evaluate side-chains
  58 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0010
   chunk 42 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
A 470 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.106239 restraints weight = 4150.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.17
r_work: 0.3091 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   3940  Z= 0.110
  Angle     :  0.482   9.671   5382  Z= 0.244
  Chirality :  0.037   0.123    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.079  43.954    535
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.72 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.08 (0.38), residues: 490
  helix:  1.82 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.23 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 382 
 TYR   0.010   0.001   TYR A 175 
 PHE   0.006   0.001   PHE A 196 
 TRP   0.008   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3940)
  covalent geometry    : angle       0.48213 ( 5382)
  hydrogen bonds       : bond        0.03814 (  277)
  hydrogen bonds       : angle       4.14881 (  819)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7472 (tt)
REVERT: A  386 PHE cc_start: 0.7855 (m-80) cc_final: 0.6605 (t80)
REVERT: A  400 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7818 (tptp)
  outliers start: 7
  outliers final: 4
  residues processed: 56
  average time/residue: 0.3917
  time to fit residues: 23.0155
Evaluate side-chains
  57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  400 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105417 restraints weight = 4121.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.17
r_work: 0.3080 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3940  Z= 0.117
  Angle     :  0.490   9.633   5382  Z= 0.249
  Chirality :  0.037   0.123    624
  Planarity :  0.003   0.027    651
  Dihedral  :  4.111  43.318    535
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.72 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  2.04 (0.38), residues: 490
  helix:  1.80 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.22 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 382 
 TYR   0.009   0.001   TYR A 175 
 PHE   0.006   0.001   PHE A 196 
 TRP   0.007   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3940)
  covalent geometry    : angle       0.49032 ( 5382)
  hydrogen bonds       : bond        0.03971 (  277)
  hydrogen bonds       : angle       4.19371 (  819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1859.18 seconds
wall clock time: 32 minutes 22.07 seconds (1942.07 seconds total)