Starting phenix.real_space_refine
on Wed Sep 17 05:25:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw1_38727/09_2025/8xw1_38727.cif"
  }
  resolution = 4.49
  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=   0.006 sd=   0.041
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      24      5.16       5
     C    3378      2.51       5
     N     826      2.21       5
     O     854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 5082
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5082
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Time building chain proxies: 1.52, per 1000 atoms: 0.30
  Number of scatterers: 5082
  At special positions: 0
  Unit cell: (92.13, 87.15, 99.6, 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      24     16.00
     O     854      8.00
     N     826      7.00
     C    3378      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: 0.53
  Conformation dependent library (CDL) restraints added in 220.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 1 sheets defined
      77.1% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.599A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 3.504A  pdb=" N   TYR A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.835A  pdb=" N   GLU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 92 through 119
      removed outlier: 4.175A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 194
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 6.155A  pdb=" N   LYS A 317 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 319 " --> pdb=" O   PRO A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 355 through 359
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.559A  pdb=" N   ALA A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.708A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 3.952A  pdb=" N   GLN A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 430  - end of helix
      removed outlier: 4.544A  pdb=" N   PHE A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 476
    Processing helix  chain 'A' and resid 477 through 490
      removed outlier: 4.486A  pdb=" N   LEU A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 512 through 524
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 553 through 559
      removed outlier: 4.381A  pdb=" N   GLU A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 589 through 612
      removed outlier: 4.316A  pdb=" N   PHE A 593 " --> pdb=" O   MET A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 654 through 659
      removed outlier: 3.717A  pdb=" N   LEU A 658 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 4.095A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 3.539A  pdb=" N   TYR A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 238
      removed outlier: 3.902A  pdb=" N   THR A 235 " --> pdb=" O   SER A 326 " (cutoff:3.500A)

    341 hydrogen bonds defined for protein.
    999 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: 0.83

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1541
        1.34 -     1.46: 994
        1.46 -     1.57: 2649
        1.57 -     1.69: 1
        1.69 -     1.81: 44
  Bond restraints: 5229
  Sorted by residual:
  bond pdb=" CG  PRO A  77 "
       pdb=" CD  PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.503  1.421  0.082 3.40e-02 8.65e+02 5.81e+00
  bond pdb=" CB  PRO A  77 "
       pdb=" CG  PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.492  1.590 -0.098 5.00e-02 4.00e+02 3.83e+00
  bond pdb=" N   TRP A 335 "
       pdb=" CA  TRP A 335 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.19e-02 7.06e+03 3.79e+00
  bond pdb=" CG  LEU A 120 "
       pdb=" CD2 LEU A 120 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.94e+00
  bond pdb=" C   TRP A 335 "
       pdb=" O   TRP A 335 "
    ideal  model  delta    sigma   weight residual
    1.236  1.221  0.015 1.15e-02 7.56e+03 1.74e+00
  ... (remaining 5224 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 6746
        1.58 -     3.17: 287
        3.17 -     4.75: 55
        4.75 -     6.34: 20
        6.34 -     7.92: 5
  Bond angle restraints: 7113
  Sorted by residual:
  angle pdb=" N   LYS A 503 "
        pdb=" CA  LYS A 503 "
        pdb=" C   LYS A 503 "
      ideal   model   delta    sigma   weight residual
     112.88  106.35    6.53 1.29e+00 6.01e-01 2.56e+01
  angle pdb=" N   PRO A  77 "
        pdb=" CD  PRO A  77 "
        pdb=" CG  PRO A  77 "
      ideal   model   delta    sigma   weight residual
     103.20   96.34    6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" CA  PRO A  77 "
        pdb=" N   PRO A  77 "
        pdb=" CD  PRO A  77 "
      ideal   model   delta    sigma   weight residual
     112.00  105.67    6.33 1.40e+00 5.10e-01 2.04e+01
  angle pdb=" C   PHE A 109 "
        pdb=" N   THR A 110 "
        pdb=" CA  THR A 110 "
      ideal   model   delta    sigma   weight residual
     119.83  116.17    3.66 1.11e+00 8.12e-01 1.09e+01
  angle pdb=" C   ASP A 552 "
        pdb=" N   LYS A 553 "
        pdb=" CA  LYS A 553 "
      ideal   model   delta    sigma   weight residual
     121.54  127.51   -5.97 1.91e+00 2.74e-01 9.78e+00
  ... (remaining 7108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 2764
       16.55 -    33.10: 239
       33.10 -    49.65: 42
       49.65 -    66.21: 9
       66.21 -    82.76: 11
  Dihedral angle restraints: 3065
    sinusoidal: 1194
      harmonic: 1871
  Sorted by residual:
  dihedral pdb=" CA  PHE A 440 "
           pdb=" C   PHE A 440 "
           pdb=" N   LEU A 441 "
           pdb=" CA  LEU A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.21  -19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLN A 340 "
           pdb=" C   GLN A 340 "
           pdb=" N   GLN A 341 "
           pdb=" CA  GLN A 341 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.68  -19.32     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  MET A  82 "
           pdb=" C   MET A  82 "
           pdb=" N   PRO A  83 "
           pdb=" CA  PRO A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 3062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 587
       0.045 -    0.091: 165
       0.091 -    0.136: 43
       0.136 -    0.181: 4
       0.181 -    0.226: 2
  Chirality restraints: 801
  Sorted by residual:
  chirality pdb=" CB  VAL A 119 "
            pdb=" CA  VAL A 119 "
            pdb=" CG1 VAL A 119 "
            pdb=" CG2 VAL A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  LYS A 536 "
            pdb=" N   LYS A 536 "
            pdb=" C   LYS A 536 "
            pdb=" CB  LYS A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CA  GLU A 311 "
            pdb=" N   GLU A 311 "
            pdb=" C   GLU A 311 "
            pdb=" CB  GLU A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  ... (remaining 798 not shown)

  Planarity restraints: 882
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  76 "    0.047 5.00e-02 4.00e+02   6.81e-02 7.43e+00
        pdb=" N   PRO A  77 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 307 "    0.014 2.00e-02 2.50e+03   2.70e-02 7.30e+00
        pdb=" C   LYS A 307 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS A 307 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU A 308 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 352 "    0.015 2.00e-02 2.50e+03   1.12e-02 3.13e+00
        pdb=" CG  TRP A 352 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 352 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 352 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 352 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 352 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 352 "    0.006 2.00e-02 2.50e+03
  ... (remaining 879 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 144
        2.69 -     3.24: 5891
        3.24 -     3.80: 8715
        3.80 -     4.35: 10301
        4.35 -     4.90: 16226
  Nonbonded interactions: 41277
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OE1 GLU A  78 "
            pdb=" NZ  LYS A  81 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" O   PHE A 224 "
            pdb=" ND2 ASN A 228 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   TRP A 335 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   LEU A 635 "
            pdb=" OG  SER A 638 "
     model   vdw
     2.234 3.040
  ... (remaining 41272 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 group one per residue
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:             1.480
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.270
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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   0.098   5229  Z= 0.250
  Angle     :  0.821   7.921   7113  Z= 0.465
  Chirality :  0.046   0.226    801
  Planarity :  0.005   0.068    882
  Dihedral  : 14.015  82.757   1849
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 20.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.95 %
    Favored  : 98.87 %
  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: -0.07 (0.33), residues: 624
  helix:  0.75 (0.25), residues: 417
  sheet: -2.19 (1.07), residues: 16
  loop : -1.55 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 462 
 TYR   0.024   0.002   TYR A 469 
 PHE   0.023   0.002   PHE A 437 
 TRP   0.029   0.002   TRP A 352 
 HIS   0.004   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 5229)
  covalent geometry    : angle       0.82088 ( 7113)
  hydrogen bonds       : bond        0.12918 (  341)
  hydrogen bonds       : angle       6.26730 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 TYR cc_start: 0.8095 (m-80) cc_final: 0.6785 (m-80)
REVERT: A   82 MET cc_start: 0.9014 (tpt) cc_final: 0.8787 (tpp)
REVERT: A  109 PHE cc_start: 0.9600 (m-10) cc_final: 0.9385 (m-10)
REVERT: A  178 MET cc_start: 0.9286 (ppp) cc_final: 0.9031 (ppp)
REVERT: A  180 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9069 (tp30)
REVERT: A  262 TYR cc_start: 0.9429 (m-80) cc_final: 0.8995 (m-80)
REVERT: A  305 ILE cc_start: 0.9548 (pt) cc_final: 0.9301 (pt)
REVERT: A  355 GLU cc_start: 0.9432 (tp30) cc_final: 0.9123 (tp30)
REVERT: A  437 PHE cc_start: 0.8999 (m-80) cc_final: 0.8594 (m-80)
REVERT: A  440 PHE cc_start: 0.8716 (m-10) cc_final: 0.8451 (t80)
REVERT: A  461 GLU cc_start: 0.9164 (tp30) cc_final: 0.8754 (mm-30)
REVERT: A  475 ASN cc_start: 0.9007 (m110) cc_final: 0.8642 (m110)
REVERT: A  511 MET cc_start: 0.9194 (mmp) cc_final: 0.8965 (mmm)
REVERT: A  532 ILE cc_start: 0.9414 (tt) cc_final: 0.9171 (tt)
REVERT: A  677 GLU cc_start: 0.8620 (pt0) cc_final: 0.8376 (pt0)
REVERT: A  710 ASN cc_start: 0.9388 (m-40) cc_final: 0.9166 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0571
  time to fit residues: 13.9826
Evaluate side-chains
  136 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 229 HIS
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 ASN
A 397 GLN
A 426 GLN
A 574 GLN
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.080283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.060721 restraints weight = 17990.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.063187 restraints weight = 10052.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.064938 restraints weight = 6664.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.065971 restraints weight = 4943.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.067047 restraints weight = 4011.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5229  Z= 0.146
  Angle     :  0.662   8.170   7113  Z= 0.335
  Chirality :  0.043   0.260    801
  Planarity :  0.005   0.038    882
  Dihedral  :  4.707  18.406    680
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  3.78 %
    Favored  : 95.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.35), residues: 624
  helix:  1.45 (0.25), residues: 422
  sheet: -2.00 (1.09), residues: 16
  loop : -1.44 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 309 
 TYR   0.014   0.001   TYR A  98 
 PHE   0.026   0.002   PHE A 428 
 TRP   0.016   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5229)
  covalent geometry    : angle       0.66156 ( 7113)
  hydrogen bonds       : bond        0.04272 (  341)
  hydrogen bonds       : angle       5.04987 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9250 (m-30) cc_final: 0.8944 (m-30)
REVERT: A   82 MET cc_start: 0.9141 (tpt) cc_final: 0.8882 (tpt)
REVERT: A  178 MET cc_start: 0.9249 (ppp) cc_final: 0.9005 (ppp)
REVERT: A  180 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9110 (tp30)
REVERT: A  262 TYR cc_start: 0.9434 (m-80) cc_final: 0.9041 (m-80)
REVERT: A  309 ARG cc_start: 0.8870 (mmp80) cc_final: 0.8515 (mmp80)
REVERT: A  355 GLU cc_start: 0.9331 (tp30) cc_final: 0.9050 (tp30)
REVERT: A  368 TYR cc_start: 0.8766 (t80) cc_final: 0.8291 (t80)
REVERT: A  437 PHE cc_start: 0.8978 (m-80) cc_final: 0.8587 (m-80)
REVERT: A  461 GLU cc_start: 0.9272 (tp30) cc_final: 0.8652 (mm-30)
REVERT: A  476 VAL cc_start: 0.9386 (t) cc_final: 0.9161 (t)
REVERT: A  511 MET cc_start: 0.9240 (mmp) cc_final: 0.8952 (mmm)
REVERT: A  540 MET cc_start: 0.9621 (mmp) cc_final: 0.9266 (mmp)
REVERT: A  576 TYR cc_start: 0.8702 (m-10) cc_final: 0.8488 (m-10)
REVERT: A  613 TYR cc_start: 0.9317 (m-80) cc_final: 0.8692 (m-80)
REVERT: A  661 LEU cc_start: 0.9787 (mt) cc_final: 0.9220 (mt)
REVERT: A  677 GLU cc_start: 0.8565 (pt0) cc_final: 0.8317 (pt0)
REVERT: A  689 MET cc_start: 0.9489 (mmp) cc_final: 0.9264 (mmm)
REVERT: A  690 MET cc_start: 0.9328 (mmt) cc_final: 0.8960 (tpt)
REVERT: A  710 ASN cc_start: 0.9435 (m-40) cc_final: 0.9227 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 186
  average time/residue: 0.0569
  time to fit residues: 14.5246
Evaluate side-chains
  142 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0070
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
A 574 GLN
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.082841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.062986 restraints weight = 17418.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.065642 restraints weight = 9573.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.067470 restraints weight = 6293.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.068702 restraints weight = 4626.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.069494 restraints weight = 3698.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5229  Z= 0.128
  Angle     :  0.650  11.325   7113  Z= 0.325
  Chirality :  0.042   0.182    801
  Planarity :  0.004   0.038    882
  Dihedral  :  4.476  18.065    680
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.02 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.80 (0.35), residues: 624
  helix:  1.44 (0.26), residues: 434
  sheet: -1.64 (1.17), residues: 16
  loop : -1.57 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 309 
 TYR   0.007   0.001   TYR A  98 
 PHE   0.023   0.002   PHE A 717 
 TRP   0.022   0.001   TRP A 624 
 HIS   0.006   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5229)
  covalent geometry    : angle       0.65037 ( 7113)
  hydrogen bonds       : bond        0.04076 (  341)
  hydrogen bonds       : angle       4.82690 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9204 (m-30) cc_final: 0.8863 (m-30)
REVERT: A   82 MET cc_start: 0.9108 (tpt) cc_final: 0.8863 (tpt)
REVERT: A  178 MET cc_start: 0.9204 (ppp) cc_final: 0.8881 (ppp)
REVERT: A  262 TYR cc_start: 0.9485 (m-80) cc_final: 0.9235 (m-80)
REVERT: A  298 ILE cc_start: 0.9677 (mm) cc_final: 0.9475 (pt)
REVERT: A  355 GLU cc_start: 0.9327 (tp30) cc_final: 0.9000 (tp30)
REVERT: A  396 VAL cc_start: 0.9680 (t) cc_final: 0.9423 (t)
REVERT: A  399 LEU cc_start: 0.9716 (mt) cc_final: 0.9447 (mt)
REVERT: A  437 PHE cc_start: 0.9059 (m-80) cc_final: 0.8518 (m-80)
REVERT: A  440 PHE cc_start: 0.8663 (m-10) cc_final: 0.8443 (t80)
REVERT: A  461 GLU cc_start: 0.9326 (tp30) cc_final: 0.8625 (mm-30)
REVERT: A  476 VAL cc_start: 0.9380 (t) cc_final: 0.9156 (t)
REVERT: A  511 MET cc_start: 0.9258 (mmp) cc_final: 0.8945 (mmm)
REVERT: A  540 MET cc_start: 0.9585 (mmp) cc_final: 0.9220 (mmp)
REVERT: A  613 TYR cc_start: 0.9268 (m-80) cc_final: 0.8604 (m-80)
REVERT: A  682 ARG cc_start: 0.8383 (mpt-90) cc_final: 0.7917 (ttm110)
REVERT: A  689 MET cc_start: 0.9500 (mmp) cc_final: 0.9255 (mmm)
REVERT: A  690 MET cc_start: 0.9339 (mmt) cc_final: 0.8966 (tpt)
REVERT: A  710 ASN cc_start: 0.9397 (m-40) cc_final: 0.9165 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0539
  time to fit residues: 13.1831
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.081787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.063171 restraints weight = 17291.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065697 restraints weight = 9361.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.067418 restraints weight = 6086.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.068784 restraints weight = 4477.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.069708 restraints weight = 3486.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5229  Z= 0.119
  Angle     :  0.603   7.382   7113  Z= 0.305
  Chirality :  0.041   0.184    801
  Planarity :  0.004   0.042    882
  Dihedral  :  4.331  17.669    680
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.78 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.35), residues: 624
  helix:  1.70 (0.26), residues: 423
  sheet: -1.60 (1.17), residues: 16
  loop : -1.19 (0.48), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.009   0.001   TYR A  98 
 PHE   0.017   0.001   PHE A 428 
 TRP   0.007   0.001   TRP A 348 
 HIS   0.004   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5229)
  covalent geometry    : angle       0.60339 ( 7113)
  hydrogen bonds       : bond        0.03725 (  341)
  hydrogen bonds       : angle       4.65495 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9260 (m-30) cc_final: 0.8898 (m-30)
REVERT: A  178 MET cc_start: 0.9168 (ppp) cc_final: 0.8815 (ppp)
REVERT: A  180 GLU cc_start: 0.9079 (tp30) cc_final: 0.8676 (tp30)
REVERT: A  298 ILE cc_start: 0.9649 (mm) cc_final: 0.9440 (pt)
REVERT: A  355 GLU cc_start: 0.9330 (tp30) cc_final: 0.8818 (tp30)
REVERT: A  396 VAL cc_start: 0.9668 (t) cc_final: 0.9275 (t)
REVERT: A  399 LEU cc_start: 0.9732 (mt) cc_final: 0.9412 (mt)
REVERT: A  437 PHE cc_start: 0.9092 (m-80) cc_final: 0.8356 (m-80)
REVERT: A  445 LEU cc_start: 0.9740 (mt) cc_final: 0.9537 (mt)
REVERT: A  461 GLU cc_start: 0.9306 (tp30) cc_final: 0.8612 (mm-30)
REVERT: A  469 TYR cc_start: 0.9540 (t80) cc_final: 0.9317 (t80)
REVERT: A  476 VAL cc_start: 0.9394 (t) cc_final: 0.9194 (t)
REVERT: A  511 MET cc_start: 0.9226 (mmp) cc_final: 0.8913 (mmm)
REVERT: A  540 MET cc_start: 0.9566 (mmp) cc_final: 0.9229 (mmp)
REVERT: A  613 TYR cc_start: 0.9231 (m-80) cc_final: 0.8545 (m-80)
REVERT: A  677 GLU cc_start: 0.8631 (pt0) cc_final: 0.8402 (pt0)
REVERT: A  682 ARG cc_start: 0.8438 (mpt-90) cc_final: 0.7974 (ttm110)
REVERT: A  690 MET cc_start: 0.9286 (mmt) cc_final: 0.8931 (tpt)
REVERT: A  710 ASN cc_start: 0.9357 (m-40) cc_final: 0.9105 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0559
  time to fit residues: 13.5228
Evaluate side-chains
  136 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
A 363 ASN
A 397 GLN
A 615 GLN
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.081148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.062163 restraints weight = 17385.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.064713 restraints weight = 9399.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066538 restraints weight = 6123.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.067677 restraints weight = 4457.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.068690 restraints weight = 3537.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5229  Z= 0.132
  Angle     :  0.598   7.513   7113  Z= 0.306
  Chirality :  0.041   0.182    801
  Planarity :  0.004   0.045    882
  Dihedral  :  4.262  18.241    680
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  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:  1.21 (0.35), residues: 624
  helix:  1.70 (0.25), residues: 424
  sheet: -1.88 (1.32), residues: 11
  loop : -1.12 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 198 
 TYR   0.008   0.001   TYR A 294 
 PHE   0.017   0.001   PHE A 428 
 TRP   0.013   0.001   TRP A  75 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5229)
  covalent geometry    : angle       0.59764 ( 7113)
  hydrogen bonds       : bond        0.03736 (  341)
  hydrogen bonds       : angle       4.63202 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9320 (m-30) cc_final: 0.8963 (m-30)
REVERT: A  165 MET cc_start: 0.9402 (mmp) cc_final: 0.9150 (mmp)
REVERT: A  180 GLU cc_start: 0.9090 (tp30) cc_final: 0.8718 (tp30)
REVERT: A  262 TYR cc_start: 0.9412 (m-80) cc_final: 0.9116 (m-80)
REVERT: A  378 MET cc_start: 0.8153 (mtt) cc_final: 0.7906 (mtt)
REVERT: A  437 PHE cc_start: 0.9076 (m-80) cc_final: 0.8202 (m-80)
REVERT: A  461 GLU cc_start: 0.9275 (tp30) cc_final: 0.8923 (tp30)
REVERT: A  469 TYR cc_start: 0.9600 (t80) cc_final: 0.9320 (t80)
REVERT: A  511 MET cc_start: 0.9213 (mmp) cc_final: 0.8903 (mmm)
REVERT: A  540 MET cc_start: 0.9537 (mmp) cc_final: 0.9209 (mmp)
REVERT: A  677 GLU cc_start: 0.8643 (pt0) cc_final: 0.8422 (pt0)
REVERT: A  682 ARG cc_start: 0.8528 (mpt-90) cc_final: 0.8012 (ttm110)
REVERT: A  710 ASN cc_start: 0.9340 (m-40) cc_final: 0.9089 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0515
  time to fit residues: 12.0841
Evaluate side-chains
  127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
A 615 GLN
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.082960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.063460 restraints weight = 17539.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.066124 restraints weight = 9638.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.068003 restraints weight = 6337.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.069189 restraints weight = 4642.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.070208 restraints weight = 3716.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5229  Z= 0.124
  Angle     :  0.631   8.960   7113  Z= 0.318
  Chirality :  0.041   0.185    801
  Planarity :  0.005   0.048    882
  Dihedral  :  4.253  17.948    680
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.65 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.35), residues: 624
  helix:  1.65 (0.25), residues: 424
  sheet: -1.72 (1.33), residues: 11
  loop : -1.05 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 198 
 TYR   0.006   0.001   TYR A 167 
 PHE   0.017   0.001   PHE A 428 
 TRP   0.012   0.001   TRP A  75 
 HIS   0.010   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5229)
  covalent geometry    : angle       0.63062 ( 7113)
  hydrogen bonds       : bond        0.03702 (  341)
  hydrogen bonds       : angle       4.59525 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9317 (m-30) cc_final: 0.8960 (m-30)
REVERT: A   82 MET cc_start: 0.9094 (tpt) cc_final: 0.8873 (tpp)
REVERT: A  165 MET cc_start: 0.9381 (mmp) cc_final: 0.9124 (mmp)
REVERT: A  180 GLU cc_start: 0.9095 (tp30) cc_final: 0.8728 (tp30)
REVERT: A  262 TYR cc_start: 0.9449 (m-80) cc_final: 0.9100 (m-80)
REVERT: A  320 MET cc_start: 0.8668 (tpt) cc_final: 0.8453 (ttt)
REVERT: A  378 MET cc_start: 0.8231 (mtt) cc_final: 0.8015 (mmm)
REVERT: A  399 LEU cc_start: 0.9721 (mt) cc_final: 0.9406 (mt)
REVERT: A  437 PHE cc_start: 0.9079 (m-80) cc_final: 0.8172 (m-80)
REVERT: A  445 LEU cc_start: 0.9704 (mt) cc_final: 0.9477 (mt)
REVERT: A  448 MET cc_start: 0.9476 (mmm) cc_final: 0.9239 (tpt)
REVERT: A  461 GLU cc_start: 0.9276 (tp30) cc_final: 0.8918 (tp30)
REVERT: A  469 TYR cc_start: 0.9606 (t80) cc_final: 0.9298 (t80)
REVERT: A  511 MET cc_start: 0.9224 (mmp) cc_final: 0.8888 (mmm)
REVERT: A  540 MET cc_start: 0.9514 (mmp) cc_final: 0.9130 (tpt)
REVERT: A  613 TYR cc_start: 0.8926 (m-80) cc_final: 0.8315 (m-80)
REVERT: A  682 ARG cc_start: 0.8548 (mpt-90) cc_final: 0.8100 (ttm110)
REVERT: A  689 MET cc_start: 0.9492 (mmp) cc_final: 0.9291 (mmm)
REVERT: A  710 ASN cc_start: 0.9322 (m-40) cc_final: 0.9091 (m-40)
  outliers start: 1
  outliers final: 1
  residues processed: 173
  average time/residue: 0.0536
  time to fit residues: 12.9768
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 35 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0060
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.083728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.063690 restraints weight = 17331.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066354 restraints weight = 9781.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.068270 restraints weight = 6541.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.069522 restraints weight = 4831.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.070544 restraints weight = 3864.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5229  Z= 0.124
  Angle     :  0.632   7.982   7113  Z= 0.318
  Chirality :  0.041   0.182    801
  Planarity :  0.005   0.049    882
  Dihedral  :  4.202  17.374    680
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  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:  1.23 (0.35), residues: 624
  helix:  1.68 (0.26), residues: 425
  sheet: -1.53 (1.48), residues: 10
  loop : -1.04 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 309 
 TYR   0.011   0.001   TYR A 613 
 PHE   0.019   0.001   PHE A  19 
 TRP   0.015   0.001   TRP A  75 
 HIS   0.009   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5229)
  covalent geometry    : angle       0.63171 ( 7113)
  hydrogen bonds       : bond        0.03694 (  341)
  hydrogen bonds       : angle       4.59598 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9322 (m-30) cc_final: 0.8950 (m-30)
REVERT: A   97 VAL cc_start: 0.9685 (t) cc_final: 0.9460 (p)
REVERT: A  165 MET cc_start: 0.9389 (mmp) cc_final: 0.9134 (mmp)
REVERT: A  178 MET cc_start: 0.9175 (ppp) cc_final: 0.8799 (ppp)
REVERT: A  180 GLU cc_start: 0.9113 (tp30) cc_final: 0.8743 (tp30)
REVERT: A  262 TYR cc_start: 0.9431 (m-80) cc_final: 0.8856 (m-80)
REVERT: A  320 MET cc_start: 0.8718 (tpt) cc_final: 0.8468 (ttt)
REVERT: A  378 MET cc_start: 0.8238 (mtt) cc_final: 0.7909 (mtt)
REVERT: A  437 PHE cc_start: 0.9104 (m-10) cc_final: 0.8190 (m-80)
REVERT: A  444 ILE cc_start: 0.9516 (mp) cc_final: 0.9295 (mp)
REVERT: A  461 GLU cc_start: 0.9249 (tp30) cc_final: 0.8904 (tp30)
REVERT: A  469 TYR cc_start: 0.9610 (t80) cc_final: 0.9186 (t80)
REVERT: A  511 MET cc_start: 0.9190 (mmp) cc_final: 0.8838 (mmm)
REVERT: A  540 MET cc_start: 0.9500 (mmp) cc_final: 0.9125 (tpt)
REVERT: A  613 TYR cc_start: 0.9019 (m-80) cc_final: 0.8432 (m-80)
REVERT: A  677 GLU cc_start: 0.8620 (pt0) cc_final: 0.8339 (pt0)
REVERT: A  682 ARG cc_start: 0.8562 (mpt-90) cc_final: 0.8045 (ttm110)
REVERT: A  689 MET cc_start: 0.9523 (mmp) cc_final: 0.9303 (mmm)
REVERT: A  690 MET cc_start: 0.9309 (mmt) cc_final: 0.8987 (tpt)
REVERT: A  710 ASN cc_start: 0.9305 (m-40) cc_final: 0.9085 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0504
  time to fit residues: 11.9254
Evaluate side-chains
  127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.083487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.064019 restraints weight = 17330.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.066658 restraints weight = 9703.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.068483 restraints weight = 6446.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.069837 restraints weight = 4772.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.070597 restraints weight = 3791.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5229  Z= 0.124
  Angle     :  0.634   7.814   7113  Z= 0.318
  Chirality :  0.042   0.189    801
  Planarity :  0.005   0.049    882
  Dihedral  :  4.175  16.977    680
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  1.11 (0.35), residues: 624
  helix:  1.56 (0.26), residues: 431
  sheet: -1.48 (1.52), residues: 10
  loop : -1.09 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 158 
 TYR   0.012   0.001   TYR A  98 
 PHE   0.017   0.001   PHE A  19 
 TRP   0.015   0.001   TRP A  75 
 HIS   0.008   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5229)
  covalent geometry    : angle       0.63418 ( 7113)
  hydrogen bonds       : bond        0.03689 (  341)
  hydrogen bonds       : angle       4.58717 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9329 (m-30) cc_final: 0.8982 (m-30)
REVERT: A  165 MET cc_start: 0.9371 (mmp) cc_final: 0.9116 (mmp)
REVERT: A  178 MET cc_start: 0.9160 (ppp) cc_final: 0.8795 (ppp)
REVERT: A  180 GLU cc_start: 0.9081 (tp30) cc_final: 0.8763 (tp30)
REVERT: A  262 TYR cc_start: 0.9425 (m-80) cc_final: 0.8884 (m-80)
REVERT: A  320 MET cc_start: 0.8665 (tpt) cc_final: 0.8432 (ttt)
REVERT: A  378 MET cc_start: 0.8279 (mtt) cc_final: 0.7944 (mtt)
REVERT: A  437 PHE cc_start: 0.9107 (m-10) cc_final: 0.8214 (m-80)
REVERT: A  461 GLU cc_start: 0.9236 (tp30) cc_final: 0.8877 (tp30)
REVERT: A  469 TYR cc_start: 0.9670 (t80) cc_final: 0.9224 (t80)
REVERT: A  511 MET cc_start: 0.9165 (mmp) cc_final: 0.8810 (mmm)
REVERT: A  540 MET cc_start: 0.9482 (mmp) cc_final: 0.9122 (tpt)
REVERT: A  579 LEU cc_start: 0.9696 (mt) cc_final: 0.9444 (mt)
REVERT: A  613 TYR cc_start: 0.9026 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  677 GLU cc_start: 0.8534 (pt0) cc_final: 0.8274 (pt0)
REVERT: A  682 ARG cc_start: 0.8565 (mpt-90) cc_final: 0.8032 (ttm110)
REVERT: A  690 MET cc_start: 0.9293 (mmt) cc_final: 0.8975 (tpt)
REVERT: A  710 ASN cc_start: 0.9291 (m-40) cc_final: 0.9075 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0531
  time to fit residues: 12.4227
Evaluate side-chains
  130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.082935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.063623 restraints weight = 17475.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.066285 restraints weight = 9706.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.068001 restraints weight = 6403.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.069422 restraints weight = 4797.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.070275 restraints weight = 3781.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5229  Z= 0.122
  Angle     :  0.639   8.711   7113  Z= 0.318
  Chirality :  0.041   0.181    801
  Planarity :  0.005   0.049    882
  Dihedral  :  4.150  16.483    680
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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:  1.06 (0.35), residues: 624
  helix:  1.51 (0.26), residues: 431
  sheet: -1.36 (1.51), residues: 10
  loop : -1.11 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 330 
 TYR   0.009   0.001   TYR A 613 
 PHE   0.018   0.001   PHE A  19 
 TRP   0.016   0.001   TRP A  75 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5229)
  covalent geometry    : angle       0.63856 ( 7113)
  hydrogen bonds       : bond        0.03644 (  341)
  hydrogen bonds       : angle       4.59435 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9358 (m-30) cc_final: 0.8679 (t0)
REVERT: A  165 MET cc_start: 0.9383 (mmp) cc_final: 0.9132 (mmp)
REVERT: A  178 MET cc_start: 0.9130 (ppp) cc_final: 0.8772 (ppp)
REVERT: A  180 GLU cc_start: 0.9100 (tp30) cc_final: 0.8776 (tp30)
REVERT: A  188 ARG cc_start: 0.9311 (ttt-90) cc_final: 0.8513 (ttt180)
REVERT: A  262 TYR cc_start: 0.9436 (m-80) cc_final: 0.8892 (m-80)
REVERT: A  320 MET cc_start: 0.8649 (tpt) cc_final: 0.8385 (ttt)
REVERT: A  378 MET cc_start: 0.8287 (mtt) cc_final: 0.7906 (mtt)
REVERT: A  437 PHE cc_start: 0.9097 (m-10) cc_final: 0.8183 (m-80)
REVERT: A  445 LEU cc_start: 0.9683 (mt) cc_final: 0.9468 (mt)
REVERT: A  461 GLU cc_start: 0.9225 (tp30) cc_final: 0.8886 (tp30)
REVERT: A  469 TYR cc_start: 0.9684 (t80) cc_final: 0.9242 (t80)
REVERT: A  511 MET cc_start: 0.9192 (mmp) cc_final: 0.8817 (mmm)
REVERT: A  540 MET cc_start: 0.9483 (mmp) cc_final: 0.9125 (tpt)
REVERT: A  579 LEU cc_start: 0.9700 (mt) cc_final: 0.9442 (mt)
REVERT: A  613 TYR cc_start: 0.9046 (m-80) cc_final: 0.8339 (m-80)
REVERT: A  677 GLU cc_start: 0.8586 (pt0) cc_final: 0.8305 (pt0)
REVERT: A  682 ARG cc_start: 0.8590 (mpt-90) cc_final: 0.8068 (ttm110)
REVERT: A  689 MET cc_start: 0.9493 (mmp) cc_final: 0.9275 (mmp)
REVERT: A  710 ASN cc_start: 0.9268 (m-40) cc_final: 0.9038 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0572
  time to fit residues: 13.7022
Evaluate side-chains
  134 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 62 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.083271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.064280 restraints weight = 17260.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.066966 restraints weight = 9505.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.068837 restraints weight = 6225.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.070139 restraints weight = 4536.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.070993 restraints weight = 3569.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5229  Z= 0.123
  Angle     :  0.630   8.124   7113  Z= 0.318
  Chirality :  0.041   0.184    801
  Planarity :  0.004   0.050    882
  Dihedral  :  4.134  16.477    680
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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:  1.05 (0.35), residues: 624
  helix:  1.47 (0.26), residues: 432
  sheet: -1.26 (1.54), residues: 10
  loop : -1.03 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.009   0.001   TYR A 613 
 PHE   0.017   0.001   PHE A  19 
 TRP   0.017   0.001   TRP A  75 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5229)
  covalent geometry    : angle       0.62987 ( 7113)
  hydrogen bonds       : bond        0.03637 (  341)
  hydrogen bonds       : angle       4.62789 (  999)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9349 (m-30) cc_final: 0.8672 (t0)
REVERT: A  165 MET cc_start: 0.9382 (mmp) cc_final: 0.9124 (mmp)
REVERT: A  178 MET cc_start: 0.9126 (ppp) cc_final: 0.8767 (ppp)
REVERT: A  180 GLU cc_start: 0.9070 (tp30) cc_final: 0.8766 (tp30)
REVERT: A  188 ARG cc_start: 0.9373 (ttt-90) cc_final: 0.8987 (ttt180)
REVERT: A  262 TYR cc_start: 0.9437 (m-80) cc_final: 0.9051 (m-80)
REVERT: A  320 MET cc_start: 0.8645 (tpt) cc_final: 0.8272 (ttt)
REVERT: A  378 MET cc_start: 0.8190 (mtt) cc_final: 0.7942 (mtt)
REVERT: A  437 PHE cc_start: 0.9104 (m-10) cc_final: 0.8185 (m-80)
REVERT: A  445 LEU cc_start: 0.9668 (mt) cc_final: 0.9460 (mt)
REVERT: A  446 MET cc_start: 0.8854 (tpt) cc_final: 0.8423 (tpp)
REVERT: A  461 GLU cc_start: 0.9216 (tp30) cc_final: 0.8902 (tp30)
REVERT: A  469 TYR cc_start: 0.9678 (t80) cc_final: 0.9241 (t80)
REVERT: A  511 MET cc_start: 0.9157 (mmp) cc_final: 0.8806 (mmm)
REVERT: A  540 MET cc_start: 0.9476 (mmp) cc_final: 0.9124 (tpt)
REVERT: A  579 LEU cc_start: 0.9702 (mt) cc_final: 0.9430 (mt)
REVERT: A  613 TYR cc_start: 0.9012 (m-80) cc_final: 0.8305 (m-80)
REVERT: A  677 GLU cc_start: 0.8605 (pt0) cc_final: 0.8283 (pt0)
REVERT: A  710 ASN cc_start: 0.9279 (m-40) cc_final: 0.8984 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0581
  time to fit residues: 13.8699
Evaluate side-chains
  134 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 29 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 397 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.084123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.064300 restraints weight = 17467.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.066997 restraints weight = 9856.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.068651 restraints weight = 6572.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.070118 restraints weight = 4987.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.071079 restraints weight = 3931.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5229  Z= 0.124
  Angle     :  0.658   8.160   7113  Z= 0.328
  Chirality :  0.041   0.163    801
  Planarity :  0.005   0.049    882
  Dihedral  :  4.113  16.422    680
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  0.98 (0.35), residues: 624
  helix:  1.47 (0.26), residues: 431
  sheet: -1.02 (1.58), residues: 10
  loop : -1.23 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 682 
 TYR   0.017   0.001   TYR A 712 
 PHE   0.021   0.001   PHE A 389 
 TRP   0.017   0.001   TRP A  75 
 HIS   0.006   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5229)
  covalent geometry    : angle       0.65815 ( 7113)
  hydrogen bonds       : bond        0.03662 (  341)
  hydrogen bonds       : angle       4.65345 (  999)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 981.30 seconds
wall clock time: 17 minutes 41.53 seconds (1061.53 seconds total)