Starting phenix.real_space_refine
on Wed Sep 17 03:37:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u5a_63867/09_2025/9u5a_63867_trim.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.090
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      26      5.16       5
     C    2149      2.51       5
     N     537      2.21       5
     O     556      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3268
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3243
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 20, 'TRANS': 411}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 54
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'ZWY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.21, per 1000 atoms: 0.37
  Number of scatterers: 3268
  At special positions: 0
  Unit cell: (88.54, 58.716, 77.356, 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      26     16.00
     O     556      8.00
     N     537      7.00
     C    2149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " distance=2.04

  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: 0.39
  Conformation dependent library (CDL) restraints added in 82.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  800

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 1 sheets defined
      83.8% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 17 through 36
      removed outlier: 3.678A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      Proline residue:  A  27  - end of helix
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 37 through 40
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 68 through 74
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 140 through 165
      removed outlier: 4.216A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 187
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 192 through 221
      removed outlier: 3.544A  pdb=" N   GLY A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 252
      removed outlier: 4.189A  pdb=" N   ALA A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 264 through 272
      removed outlier: 4.178A  pdb=" N   ALA A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 287
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 346 through 365
      removed outlier: 4.099A  pdb=" N   GLY A 362 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 373 through 399
      removed outlier: 3.511A  pdb=" N   LEU A 377 " --> pdb=" O   ASP A 373 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 422
      removed outlier: 3.683A  pdb=" N   GLN A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 454
    Processing helix  chain 'A' and resid 464 through 478
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.674A  pdb=" N   ILE A 482 " --> pdb=" O   MET A 478 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 478 through 483'
    Processing helix  chain 'A' and resid 484 through 487
      removed outlier: 3.872A  pdb=" N   GLN A 487 " --> pdb=" O   MET A 484 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 484 through 487'
    Processing helix  chain 'A' and resid 491 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88

    241 hydrogen bonds defined for protein.
    714 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: 0.52

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 485
        1.32 -     1.44: 920
        1.44 -     1.56: 1898
        1.56 -     1.68: 2
        1.68 -     1.81: 39
  Bond restraints: 3344
  Sorted by residual:
  bond pdb=" O22 ZWY A 601 "
       pdb=" S21 ZWY A 601 "
    ideal  model  delta    sigma   weight residual
    1.457  1.674 -0.217 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" C   ILE A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.386 -0.057 1.18e-02 7.18e+03 2.29e+01
  bond pdb=" C   ILE A 404 "
       pdb=" O   ILE A 404 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.13e-02 7.83e+03 1.48e+01
  bond pdb=" C   LEU A 414 "
       pdb=" O   LEU A 414 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.17e-02 7.31e+03 1.38e+01
  bond pdb=" C   LEU A 377 "
       pdb=" O   LEU A 377 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.042 1.17e-02 7.31e+03 1.31e+01
  ... (remaining 3339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 4254
        2.36 -     4.71: 245
        4.71 -     7.07: 47
        7.07 -     9.42: 10
        9.42 -    11.78: 4
  Bond angle restraints: 4560
  Sorted by residual:
  angle pdb=" C   LEU A 492 "
        pdb=" N   PRO A 493 "
        pdb=" CA  PRO A 493 "
      ideal   model   delta    sigma   weight residual
     120.38  111.82    8.56 1.03e+00 9.43e-01 6.90e+01
  angle pdb=" N   ASN A  39 "
        pdb=" CA  ASN A  39 "
        pdb=" C   ASN A  39 "
      ideal   model   delta    sigma   weight residual
     113.23  104.41    8.82 1.24e+00 6.50e-01 5.06e+01
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     110.70  118.92   -8.22 1.22e+00 6.72e-01 4.54e+01
  angle pdb=" N   TRP A  93 "
        pdb=" CA  TRP A  93 "
        pdb=" C   TRP A  93 "
      ideal   model   delta    sigma   weight residual
     113.15  106.09    7.06 1.19e+00 7.06e-01 3.52e+01
  angle pdb=" N   ILE A 148 "
        pdb=" CA  ILE A 148 "
        pdb=" C   ILE A 148 "
      ideal   model   delta    sigma   weight residual
     111.00  104.92    6.08 1.09e+00 8.42e-01 3.11e+01
  ... (remaining 4555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 1816
       15.05 -    30.11: 144
       30.11 -    45.16: 28
       45.16 -    60.21: 3
       60.21 -    75.26: 3
  Dihedral angle restraints: 1994
    sinusoidal: 762
      harmonic: 1232
  Sorted by residual:
  dihedral pdb=" C   ARG A 401 "
           pdb=" N   ARG A 401 "
           pdb=" CA  ARG A 401 "
           pdb=" CB  ARG A 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.04   14.44     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" CB  CYS A  85 "
           pdb=" SG  CYS A  85 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.52   43.52     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" N   ARG A 401 "
           pdb=" C   ARG A 401 "
           pdb=" CA  ARG A 401 "
           pdb=" CB  ARG A 401 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.96  -10.16     0      2.50e+00 1.60e-01 1.65e+01
  ... (remaining 1991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 457
       0.109 -    0.217: 81
       0.217 -    0.325: 10
       0.325 -    0.434: 3
       0.434 -    0.542: 1
  Chirality restraints: 552
  Sorted by residual:
  chirality pdb=" CA  ARG A 401 "
            pdb=" N   ARG A 401 "
            pdb=" C   ARG A 401 "
            pdb=" CB  ARG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.35e+00
  chirality pdb=" CA  TYR A 165 "
            pdb=" N   TYR A 165 "
            pdb=" C   TYR A 165 "
            pdb=" CB  TYR A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  TYR A 361 "
            pdb=" N   TYR A 361 "
            pdb=" C   TYR A 361 "
            pdb=" CB  TYR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.00e+00
  ... (remaining 549 not shown)

  Planarity restraints: 552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 ZWY A 601 "   -0.038 2.00e-02 2.50e+03   4.52e-02 2.56e+01
        pdb=" C13 ZWY A 601 "    0.026 2.00e-02 2.50e+03
        pdb=" C14 ZWY A 601 "    0.074 2.00e-02 2.50e+03
        pdb=" C15 ZWY A 601 "   -0.013 2.00e-02 2.50e+03
        pdb=" C19 ZWY A 601 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  94 "   -0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   GLN A  94 "    0.068 2.00e-02 2.50e+03
        pdb=" O   GLN A  94 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   LEU A  95 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 152 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.42e+00
        pdb=" C   GLY A 152 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A 152 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A 153 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 549 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1330
        2.89 -     3.39: 3406
        3.39 -     3.89: 5643
        3.89 -     4.40: 6670
        4.40 -     4.90: 10430
  Nonbonded interactions: 27479
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 107 "
            pdb=" OG1 THR A 110 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" CE  MET A  35 "
            pdb=" O22 ZWY A 601 "
     model   vdw
     2.499 3.460
  nonbonded pdb=" N   TRP A  93 "
            pdb=" N   GLN A  94 "
     model   vdw
     2.513 2.560
  nonbonded pdb=" N   ASN A  39 "
            pdb=" N   PHE A  40 "
     model   vdw
     2.515 2.560
  nonbonded pdb=" N   THR A  23 "
            pdb=" N   PHE A  24 "
     model   vdw
     2.539 2.560
  ... (remaining 27474 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:             0.750
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
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      :  0.010   0.217   3346  Z= 0.742
  Angle     :  1.345  11.776   4564  Z= 0.894
  Chirality :  0.088   0.542    552
  Planarity :  0.008   0.057    552
  Dihedral  : 11.092  75.265   1188
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.42), residues: 418
  helix:  0.84 (0.30), residues: 322
  sheet: -3.79 (1.08), residues: 10
  loop : -1.21 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 473 
 TYR   0.021   0.003   TYR A 165 
 PHE   0.023   0.002   PHE A 211 
 TRP   0.015   0.002   TRP A 255 
 HIS   0.007   0.002   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.01034 ( 3344)
  covalent geometry    : angle       1.34262 ( 4560)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       3.15806 (    4)
  hydrogen bonds       : bond        0.20144 (  241)
  hydrogen bonds       : angle       7.27894 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  285 ILE cc_start: 0.7761 (mt) cc_final: 0.7506 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.4581
  time to fit residues: 32.7212
Evaluate side-chains
  43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 242 GLN
A 405 GLN
A 424 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.168324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137289 restraints weight = 3826.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.11
r_work: 0.3464 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3346  Z= 0.170
  Angle     :  0.623   6.614   4564  Z= 0.311
  Chirality :  0.039   0.119    552
  Planarity :  0.006   0.043    552
  Dihedral  :  6.904  84.495    513
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.12 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.43), residues: 418
  helix:  1.79 (0.29), residues: 321
  sheet: -4.34 (0.89), residues: 10
  loop :  0.16 (0.73), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 281 
 TYR   0.018   0.002   TYR A 165 
 PHE   0.014   0.002   PHE A 398 
 TRP   0.009   0.001   TRP A 175 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 3344)
  covalent geometry    : angle       0.62214 ( 4560)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       1.38031 (    4)
  hydrogen bonds       : bond        0.04850 (  241)
  hydrogen bonds       : angle       4.22008 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  285 ILE cc_start: 0.7313 (mt) cc_final: 0.7080 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 56
  average time/residue: 0.3370
  time to fit residues: 19.7208
Evaluate side-chains
  41 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  276 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.166337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.134967 restraints weight = 3950.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.18
r_work: 0.3418 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3346  Z= 0.145
  Angle     :  0.569   6.878   4564  Z= 0.278
  Chirality :  0.038   0.125    552
  Planarity :  0.005   0.038    552
  Dihedral  :  6.342  80.022    513
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.50 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.43), residues: 418
  helix:  2.19 (0.29), residues: 320
  sheet: -4.34 (0.87), residues: 10
  loop :  0.64 (0.78), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 281 
 TYR   0.013   0.002   TYR A 165 
 PHE   0.024   0.002   PHE A  24 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3344)
  covalent geometry    : angle       0.56860 ( 4560)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       1.06540 (    4)
  hydrogen bonds       : bond        0.04144 (  241)
  hydrogen bonds       : angle       3.94576 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  422 VAL cc_start: 0.8459 (t) cc_final: 0.8250 (m)
  outliers start: 7
  outliers final: 1
  residues processed: 51
  average time/residue: 0.2909
  time to fit residues: 15.6351
Evaluate side-chains
  38 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 19 optimal weight:    0.0870
   chunk 38 optimal weight:    0.0770
   chunk 34 optimal weight:    0.0870
   chunk 37 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.2094

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.168913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.137839 restraints weight = 3825.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.17
r_work: 0.3480 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3346  Z= 0.104
  Angle     :  0.512   6.586   4564  Z= 0.248
  Chirality :  0.035   0.123    552
  Planarity :  0.004   0.035    552
  Dihedral  :  6.273  84.018    513
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.07 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.00 (0.43), residues: 418
  helix:  2.57 (0.29), residues: 319
  sheet: -4.12 (0.95), residues: 10
  loop :  0.67 (0.77), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 281 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.026   0.001   PHE A  24 
 TRP   0.007   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3344)
  covalent geometry    : angle       0.51186 ( 4560)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.72985 (    4)
  hydrogen bonds       : bond        0.03408 (  241)
  hydrogen bonds       : angle       3.75172 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  398 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6213 (m-10)
  outliers start: 6
  outliers final: 1
  residues processed: 46
  average time/residue: 0.4173
  time to fit residues: 20.0340
Evaluate side-chains
  39 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  398 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0040
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 405 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.167607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.136007 restraints weight = 3898.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.18
r_work: 0.3435 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3346  Z= 0.136
  Angle     :  0.525   6.637   4564  Z= 0.253
  Chirality :  0.036   0.119    552
  Planarity :  0.004   0.036    552
  Dihedral  :  6.483  89.026    513
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.96 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.02 (0.43), residues: 418
  helix:  2.53 (0.29), residues: 319
  sheet: -4.11 (0.99), residues: 10
  loop :  0.88 (0.80), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.012   0.001   TYR A 165 
 PHE   0.013   0.001   PHE A  24 
 TRP   0.007   0.001   TRP A 255 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3344)
  covalent geometry    : angle       0.52442 ( 4560)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.88796 (    4)
  hydrogen bonds       : bond        0.03685 (  241)
  hydrogen bonds       : angle       3.78138 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  398 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6273 (m-10)
REVERT: A  495 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7472 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 46
  average time/residue: 0.4015
  time to fit residues: 19.2842
Evaluate side-chains
  43 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  495 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.161382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.128979 restraints weight = 3843.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.20
r_work: 0.3361 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3346  Z= 0.197
  Angle     :  0.580   6.726   4564  Z= 0.284
  Chirality :  0.039   0.118    552
  Planarity :  0.004   0.037    552
  Dihedral  :  6.023  78.644    513
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.96 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.43), residues: 418
  helix:  2.25 (0.29), residues: 320
  sheet: -4.06 (0.96), residues: 10
  loop :  0.95 (0.80), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  86 
 TYR   0.012   0.002   TYR A 165 
 PHE   0.016   0.002   PHE A  24 
 TRP   0.007   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 3344)
  covalent geometry    : angle       0.57876 ( 4560)
  SS BOND              : bond        0.00381 (    2)
  SS BOND              : angle       1.29784 (    4)
  hydrogen bonds       : bond        0.04401 (  241)
  hydrogen bonds       : angle       3.86576 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  398 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6376 (m-10)
  outliers start: 10
  outliers final: 3
  residues processed: 51
  average time/residue: 0.4181
  time to fit residues: 22.0798
Evaluate side-chains
  44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  505 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.164410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131935 restraints weight = 3867.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.24
r_work: 0.3406 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3346  Z= 0.137
  Angle     :  0.524   6.818   4564  Z= 0.254
  Chirality :  0.036   0.118    552
  Planarity :  0.004   0.037    552
  Dihedral  :  5.833  76.854    513
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.56 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.43), residues: 418
  helix:  2.44 (0.29), residues: 320
  sheet: -3.80 (1.02), residues: 10
  loop :  0.97 (0.81), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.015   0.001   PHE A  24 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3344)
  covalent geometry    : angle       0.52390 ( 4560)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       0.91923 (    4)
  hydrogen bonds       : bond        0.03805 (  241)
  hydrogen bonds       : angle       3.76708 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  398 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6248 (m-10)
  outliers start: 9
  outliers final: 4
  residues processed: 46
  average time/residue: 0.3872
  time to fit residues: 18.5914
Evaluate side-chains
  44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  398 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 2 optimal weight:    0.1980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.3736

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.168029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136672 restraints weight = 3896.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.24
r_work: 0.3441 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3346  Z= 0.106
  Angle     :  0.487   6.617   4564  Z= 0.238
  Chirality :  0.035   0.119    552
  Planarity :  0.004   0.036    552
  Dihedral  :  5.714  76.303    513
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.45 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.28 (0.43), residues: 418
  helix:  2.67 (0.29), residues: 321
  sheet: -3.44 (1.12), residues: 10
  loop :  1.03 (0.82), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  86 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.014   0.001   PHE A  24 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3344)
  covalent geometry    : angle       0.48627 ( 4560)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.70637 (    4)
  hydrogen bonds       : bond        0.03342 (  241)
  hydrogen bonds       : angle       3.71779 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7082 (mmt) cc_final: 0.6874 (mmm)
REVERT: A  398 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.6160 (m-10)
  outliers start: 6
  outliers final: 4
  residues processed: 49
  average time/residue: 0.3888
  time to fit residues: 19.8617
Evaluate side-chains
  44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  398 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.165642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.133629 restraints weight = 3901.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.24
r_work: 0.3420 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3346  Z= 0.127
  Angle     :  0.514   7.524   4564  Z= 0.251
  Chirality :  0.037   0.118    552
  Planarity :  0.004   0.038    552
  Dihedral  :  5.709  75.709    513
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.35 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.28 (0.43), residues: 418
  helix:  2.66 (0.29), residues: 321
  sheet: -3.19 (1.21), residues: 10
  loop :  1.05 (0.83), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  87 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.011   0.001   PHE A  24 
 TRP   0.008   0.001   TRP A  50 
 HIS   0.001   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3344)
  covalent geometry    : angle       0.51383 ( 4560)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.81276 (    4)
  hydrogen bonds       : bond        0.03626 (  241)
  hydrogen bonds       : angle       3.73297 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7186 (mmt) cc_final: 0.6985 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 45
  average time/residue: 0.3551
  time to fit residues: 16.7047
Evaluate side-chains
  44 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  385 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.165298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.132874 restraints weight = 3902.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.25
r_work: 0.3433 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3346  Z= 0.132
  Angle     :  0.521   7.658   4564  Z= 0.254
  Chirality :  0.037   0.118    552
  Planarity :  0.004   0.037    552
  Dihedral  :  5.722  75.488    513
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.35 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.44), residues: 418
  helix:  2.64 (0.29), residues: 321
  sheet: -2.97 (1.29), residues: 10
  loop :  0.98 (0.82), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  87 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.015   0.001   PHE A  24 
 TRP   0.007   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3344)
  covalent geometry    : angle       0.52049 ( 4560)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.83100 (    4)
  hydrogen bonds       : bond        0.03684 (  241)
  hydrogen bonds       : angle       3.76371 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  398 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.6071 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.4226
  time to fit residues: 20.2464
Evaluate side-chains
  45 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  398 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0070
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.2756

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.169010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.137584 restraints weight = 3907.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.23
r_work: 0.3486 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.4430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3346  Z= 0.102
  Angle     :  0.490   7.863   4564  Z= 0.240
  Chirality :  0.035   0.128    552
  Planarity :  0.004   0.037    552
  Dihedral  :  5.726  76.918    513
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 20.54 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.45 (0.44), residues: 418
  helix:  2.79 (0.29), residues: 321
  sheet: -2.91 (1.37), residues: 10
  loop :  1.04 (0.83), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  87 
 TYR   0.008   0.001   TYR A 165 
 PHE   0.011   0.001   PHE A  24 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3344)
  covalent geometry    : angle       0.48981 ( 4560)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.64405 (    4)
  hydrogen bonds       : bond        0.03261 (  241)
  hydrogen bonds       : angle       3.70331 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1196.99 seconds
wall clock time: 21 minutes 13.30 seconds (1273.30 seconds total)