Starting phenix.real_space_refine
on Tue Feb  3 13:38:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9km2_62420/02_2026/9km2_62420.map"
  }
  resolution = 3.8
  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=   0.027
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      18      5.16       5
     C    2156      2.51       5
     N     502      2.21       5
     O     550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3226
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3226
          Classifications: {'peptide': 463}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 489
          Unresolved non-hydrogen angles: 654
          Unresolved non-hydrogen dihedrals: 416
          Unresolved non-hydrogen chiralities: 53
          Planarities with less than four sites: {'TYR:plan': 8, 'ASN:plan1': 4, 'GLN:plan1': 6, 'TRP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 5, 'ASP:plan': 6, 'PHE:plan': 11, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 273
  Time building chain proxies: 1.12, per 1000 atoms: 0.35
  Number of scatterers: 3226
  At special positions: 0
  Unit cell: (68, 65.45, 74.8, 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      18     16.00
     O     550      8.00
     N     502      7.00
     C    2156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 158.7 milliseconds
  

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  860

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      70.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 221 through 232
    Processing helix  chain 'A' and resid 232 through 239
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 261 through 283
      removed outlier: 4.164A  pdb=" N   GLY A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 266 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   TYR A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 294
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.827A  pdb=" N   ALA A 301 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
    Processing helix  chain 'A' and resid 385 through 402
      removed outlier: 3.538A  pdb=" N   PHE A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 394 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   VAL A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   SER A 402 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 431
      removed outlier: 3.841A  pdb=" N   VAL A 423 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 447
    Processing helix  chain 'A' and resid 456 through 470
      removed outlier: 3.528A  pdb=" N   LYS A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 463 " --> pdb=" O   TRP A 459 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 470 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 524
      removed outlier: 4.155A  pdb=" N   VAL A 515 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY A 517 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   PHE A 518 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 546
      removed outlier: 3.567A  pdb=" N   TYR A 542 " --> pdb=" O   ALA A 538 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
    Processing helix  chain 'A' and resid 552 through 584
      removed outlier: 4.274A  pdb=" N   ALA A 556 " --> pdb=" O   SER A 552 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ILE A 557 " --> pdb=" O   PRO A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 592
      No H-bonds generated for 'chain 'A' and resid 590 through 592'
    Processing helix  chain 'A' and resid 593 through 609
      removed outlier: 4.213A  pdb=" N   PHE A 606 " --> pdb=" O   CYS A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 628
      removed outlier: 4.312A  pdb=" N   MET A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 628 " --> pdb=" O   VAL A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 646
      removed outlier: 3.548A  pdb=" N   VAL A 634 " --> pdb=" O   SER A 630 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 635 " --> pdb=" O   TYR A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 668 through 675
      removed outlier: 3.672A  pdb=" N   CYS A 672 " --> pdb=" O   PHE A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 690
      removed outlier: 3.593A  pdb=" N   THR A 679 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 719
      removed outlier: 3.909A  pdb=" N   MET A 707 " --> pdb=" O   PRO A 703 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A 708 " --> pdb=" O   THR A 704 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   MET A 709 " --> pdb=" O   TRP A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 724

    195 hydrogen bonds defined for protein.
    582 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: 0.28

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 606
        1.33 -     1.45: 830
        1.45 -     1.57: 1849
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3311
  Sorted by residual:
  bond pdb=" N   ILE A 719 "
       pdb=" CA  ILE A 719 "
    ideal  model  delta    sigma   weight residual
    1.455  1.497 -0.042 1.38e-02 5.25e+03 9.13e+00
  bond pdb=" N   VAL A 718 "
       pdb=" CA  VAL A 718 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.30e-02 5.92e+03 7.90e+00
  bond pdb=" N   VAL A 723 "
       pdb=" CA  VAL A 723 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.88e+00
  bond pdb=" N   LEU A 712 "
       pdb=" CA  LEU A 712 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.98e+00
  bond pdb=" N   ILE A 721 "
       pdb=" CA  ILE A 721 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.028 1.23e-02 6.61e+03 5.34e+00
  ... (remaining 3306 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 4314
        1.31 -     2.62: 162
        2.62 -     3.94: 42
        3.94 -     5.25: 11
        5.25 -     6.56: 3
  Bond angle restraints: 4532
  Sorted by residual:
  angle pdb=" C   GLY A 710 "
        pdb=" N   TRP A 711 "
        pdb=" CA  TRP A 711 "
      ideal   model   delta    sigma   weight residual
     120.31  113.75    6.56 1.52e+00 4.33e-01 1.86e+01
  angle pdb=" N   TRP A 711 "
        pdb=" CA  TRP A 711 "
        pdb=" C   TRP A 711 "
      ideal   model   delta    sigma   weight residual
     111.82  106.99    4.83 1.16e+00 7.43e-01 1.73e+01
  angle pdb=" N   VAL A 197 "
        pdb=" CA  VAL A 197 "
        pdb=" C   VAL A 197 "
      ideal   model   delta    sigma   weight residual
     112.98  108.28    4.70 1.25e+00 6.40e-01 1.42e+01
  angle pdb=" CA  SER A 717 "
        pdb=" C   SER A 717 "
        pdb=" O   SER A 717 "
      ideal   model   delta    sigma   weight residual
     120.90  117.22    3.68 1.03e+00 9.43e-01 1.28e+01
  angle pdb=" N   MET A 713 "
        pdb=" CA  MET A 713 "
        pdb=" C   MET A 713 "
      ideal   model   delta    sigma   weight residual
     111.07  107.26    3.81 1.07e+00 8.73e-01 1.27e+01
  ... (remaining 4527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 1644
       17.89 -    35.78: 182
       35.78 -    53.66: 62
       53.66 -    71.55: 7
       71.55 -    89.44: 1
  Dihedral angle restraints: 1896
    sinusoidal: 561
      harmonic: 1335
  Sorted by residual:
  dihedral pdb=" N   PRO A 436 "
           pdb=" CA  PRO A 436 "
           pdb=" CB  PRO A 436 "
           pdb=" CG  PRO A 436 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -119.44   89.44     1      2.00e+01 2.50e-03 2.38e+01
  dihedral pdb=" CA  PHE A 675 "
           pdb=" C   PHE A 675 "
           pdb=" N   VAL A 676 "
           pdb=" CA  VAL A 676 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.79  -17.21     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CG  ARG A 208 "
           pdb=" CD  ARG A 208 "
           pdb=" NE  ARG A 208 "
           pdb=" CZ  ARG A 208 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.78  -42.22     2      1.50e+01 4.44e-03 9.63e+00
  ... (remaining 1893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 321
       0.036 -    0.071: 156
       0.071 -    0.107: 47
       0.107 -    0.143: 8
       0.143 -    0.178: 3
  Chirality restraints: 535
  Sorted by residual:
  chirality pdb=" CA  CYS A 716 "
            pdb=" N   CYS A 716 "
            pdb=" C   CYS A 716 "
            pdb=" CB  CYS A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CA  LEU A 714 "
            pdb=" N   LEU A 714 "
            pdb=" C   LEU A 714 "
            pdb=" CB  LEU A 714 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.76e-01
  chirality pdb=" CA  MET A 713 "
            pdb=" N   MET A 713 "
            pdb=" C   MET A 713 "
            pdb=" CB  MET A 713 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 532 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 710 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   GLY A 710 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLY A 710 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TRP A 711 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 282 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   ILE A 282 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A 282 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 283 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 711 "   -0.007 2.00e-02 2.50e+03   1.53e-02 2.35e+00
        pdb=" C   TRP A 711 "    0.027 2.00e-02 2.50e+03
        pdb=" O   TRP A 711 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 712 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1119
        2.83 -     3.35: 3257
        3.35 -     3.86: 5096
        3.86 -     4.38: 5267
        4.38 -     4.90: 9245
  Nonbonded interactions: 23984
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 672 "
            pdb=" OG1 THR A 677 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER A 552 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   LEU A 641 "
            pdb=" OG  SER A 645 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" OG1 THR A 614 "
            pdb=" N   GLN A 615 "
     model   vdw
     2.421 3.120
  nonbonded pdb=" N   PRO A 595 "
            pdb=" CG  PRO A 595 "
     model   vdw
     2.442 2.816
  ... (remaining 23979 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.010
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3311  Z= 0.209
  Angle     :  0.647   6.561   4532  Z= 0.392
  Chirality :  0.045   0.178    535
  Planarity :  0.004   0.033    558
  Dihedral  : 17.222  89.441   1036
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 30.17 %
    Favored  : 67.36 %
  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 are not related in a simple way.
  whole: -1.81 (0.39), residues: 453
  helix:  0.06 (0.31), residues: 287
  sheet:  None (None), residues: 0
  loop : -3.57 (0.44), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 278 
 PHE   0.014   0.001   PHE A 445 
 TRP   0.007   0.001   TRP A 474 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3311)
  covalent geometry    : angle       0.64710 ( 4532)
  hydrogen bonds       : bond        0.18225 (  195)
  hydrogen bonds       : angle       7.28888 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.114 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
  outliers start: 7
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0320
  time to fit residues: 3.5694
Evaluate side-chains
  77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  720 TRP
Chi-restraints excluded: chain A residue  723 VAL
Chi-restraints excluded: chain A residue  724 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.204411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.185897 restraints weight = 4674.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.188312 restraints weight = 3365.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.190379 restraints weight = 2636.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.191286 restraints weight = 2209.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.192506 restraints weight = 1964.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3311  Z= 0.120
  Angle     :  0.545   5.437   4532  Z= 0.290
  Chirality :  0.041   0.123    535
  Planarity :  0.004   0.038    558
  Dihedral  :  6.002  46.515    489
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 28.93 %
    Favored  : 67.77 %
  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 are not related in a simple way.
  whole: -0.74 (0.41), residues: 453
  helix:  0.80 (0.32), residues: 298
  sheet:  None (None), residues: 0
  loop : -3.19 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.007   0.001   TYR A 279 
 PHE   0.009   0.001   PHE A 420 
 TRP   0.007   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3311)
  covalent geometry    : angle       0.54540 ( 4532)
  hydrogen bonds       : bond        0.03915 (  195)
  hydrogen bonds       : angle       4.73029 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.111 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
  outliers start: 9
  outliers final: 4
  residues processed: 88
  average time/residue: 0.0297
  time to fit residues: 3.8831
Evaluate side-chains
  80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  720 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0470
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.204841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.186555 restraints weight = 4604.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.189000 restraints weight = 3308.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.190500 restraints weight = 2612.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.192210 restraints weight = 2221.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.192974 restraints weight = 1943.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3311  Z= 0.112
  Angle     :  0.528   5.380   4532  Z= 0.278
  Chirality :  0.041   0.117    535
  Planarity :  0.004   0.043    558
  Dihedral  :  4.957  47.408    481
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 25.21 %
    Favored  : 69.83 %
  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 are not related in a simple way.
  whole: -0.59 (0.42), residues: 453
  helix:  1.00 (0.32), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.34 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.005   0.001   TYR A 211 
 PHE   0.021   0.001   PHE A 445 
 TRP   0.011   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3311)
  covalent geometry    : angle       0.52811 ( 4532)
  hydrogen bonds       : bond        0.03457 (  195)
  hydrogen bonds       : angle       4.34094 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.135 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  279 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.7219 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0319
  time to fit residues: 4.1363
Evaluate side-chains
  86 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  716 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0020
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0470
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5086

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.205753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.187564 restraints weight = 4565.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.190082 restraints weight = 3278.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.192116 restraints weight = 2564.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.193153 restraints weight = 2138.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.194288 restraints weight = 1884.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3311  Z= 0.103
  Angle     :  0.514   5.366   4532  Z= 0.269
  Chirality :  0.041   0.120    535
  Planarity :  0.004   0.040    558
  Dihedral  :  4.013  18.784    479
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.45 %
    Favored  : 68.60 %
  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 are not related in a simple way.
  whole: -0.39 (0.42), residues: 453
  helix:  1.17 (0.32), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.33 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.005   0.001   TYR A 278 
 PHE   0.011   0.001   PHE A 606 
 TRP   0.009   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3311)
  covalent geometry    : angle       0.51399 ( 4532)
  hydrogen bonds       : bond        0.03047 (  195)
  hydrogen bonds       : angle       4.12087 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.136 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  279 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7065 (t80)
REVERT: A  720 TRP cc_start: 0.7019 (m-10) cc_final: 0.6029 (m100)
  outliers start: 13
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0355
  time to fit residues: 4.6983
Evaluate side-chains
  88 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 27 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.7880

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.203059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.184607 restraints weight = 4610.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.187017 restraints weight = 3355.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.187805 restraints weight = 2648.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.189969 restraints weight = 2356.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.190817 restraints weight = 2030.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3311  Z= 0.119
  Angle     :  0.531   5.488   4532  Z= 0.279
  Chirality :  0.041   0.121    535
  Planarity :  0.004   0.042    558
  Dihedral  :  4.085  18.918    479
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.93 %
    Favored  : 67.36 %
  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 are not related in a simple way.
  whole: -0.50 (0.42), residues: 453
  helix:  1.06 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.31 (0.48), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.005   0.001   TYR A 278 
 PHE   0.010   0.001   PHE A 606 
 TRP   0.009   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3311)
  covalent geometry    : angle       0.53148 ( 4532)
  hydrogen bonds       : bond        0.03369 (  195)
  hydrogen bonds       : angle       4.29502 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.117 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  279 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7156 (t80)
REVERT: A  720 TRP cc_start: 0.7086 (m-10) cc_final: 0.6436 (m100)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0302
  time to fit residues: 3.9098
Evaluate side-chains
  86 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  716 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0040
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6792

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.203849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.185678 restraints weight = 4605.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.188054 restraints weight = 3314.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.190040 restraints weight = 2621.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.191054 restraints weight = 2200.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.192122 restraints weight = 1942.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3311  Z= 0.111
  Angle     :  0.522   5.447   4532  Z= 0.274
  Chirality :  0.041   0.121    535
  Planarity :  0.004   0.041    558
  Dihedral  :  4.018  18.446    479
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 27.27 %
    Favored  : 67.36 %
  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 are not related in a simple way.
  whole: -0.38 (0.42), residues: 453
  helix:  1.14 (0.32), residues: 298
  sheet:  None (None), residues: 0
  loop : -3.21 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.005   0.001   TYR A 279 
 PHE   0.005   0.001   PHE A 420 
 TRP   0.010   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3311)
  covalent geometry    : angle       0.52159 ( 4532)
  hydrogen bonds       : bond        0.03165 (  195)
  hydrogen bonds       : angle       4.18652 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.132 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  279 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7012 (t80)
REVERT: A  485 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7389 (mtmm)
  outliers start: 14
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0392
  time to fit residues: 4.7748
Evaluate side-chains
  87 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  485 LYS
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.198149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.179578 restraints weight = 4718.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.181881 restraints weight = 3449.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.183779 restraints weight = 2742.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.184784 restraints weight = 2317.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.185785 restraints weight = 2060.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3311  Z= 0.169
  Angle     :  0.589   5.628   4532  Z= 0.313
  Chirality :  0.043   0.129    535
  Planarity :  0.004   0.042    558
  Dihedral  :  4.440  20.475    479
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 27.27 %
    Favored  : 66.94 %
  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 are not related in a simple way.
  whole: -0.83 (0.41), residues: 453
  helix:  0.79 (0.31), residues: 297
  sheet:  None (None), residues: 0
  loop : -3.35 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 385 
 TYR   0.008   0.001   TYR A 697 
 PHE   0.013   0.001   PHE A 606 
 TRP   0.010   0.001   TRP A 300 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3311)
  covalent geometry    : angle       0.58906 ( 4532)
  hydrogen bonds       : bond        0.04039 (  195)
  hydrogen bonds       : angle       4.65959 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.139 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  485 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7288 (mtmm)
REVERT: A  668 PHE cc_start: 0.6515 (t80) cc_final: 0.6301 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0347
  time to fit residues: 4.4036
Evaluate side-chains
  91 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LYS
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.202304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.183895 restraints weight = 4684.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.186344 restraints weight = 3355.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.188282 restraints weight = 2633.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.189311 restraints weight = 2209.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.190473 restraints weight = 1951.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3311  Z= 0.115
  Angle     :  0.534   5.463   4532  Z= 0.281
  Chirality :  0.041   0.123    535
  Planarity :  0.004   0.043    558
  Dihedral  :  4.152  18.612    479
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 28.10 %
    Favored  : 66.53 %
  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 are not related in a simple way.
  whole: -0.54 (0.42), residues: 453
  helix:  1.00 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.26 (0.48), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 278 
 PHE   0.009   0.001   PHE A 606 
 TRP   0.010   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3311)
  covalent geometry    : angle       0.53378 ( 4532)
  hydrogen bonds       : bond        0.03270 (  195)
  hydrogen bonds       : angle       4.30700 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.112 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
REVERT: A  485 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7191 (mtmm)
REVERT: A  668 PHE cc_start: 0.6359 (t80) cc_final: 0.6117 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0323
  time to fit residues: 3.9948
Evaluate side-chains
  89 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  485 LYS
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   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 = 0.4185 r_free = 0.4185 target = 0.203208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.184902 restraints weight = 4656.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.187379 restraints weight = 3333.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.189437 restraints weight = 2605.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.190350 restraints weight = 2174.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.191567 restraints weight = 1935.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3311  Z= 0.112
  Angle     :  0.530   5.438   4532  Z= 0.278
  Chirality :  0.041   0.121    535
  Planarity :  0.004   0.043    558
  Dihedral  :  4.049  18.923    479
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 28.93 %
    Favored  : 66.12 %
  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 are not related in a simple way.
  whole: -0.45 (0.42), residues: 453
  helix:  1.07 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.22 (0.48), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 278 
 PHE   0.008   0.001   PHE A 606 
 TRP   0.010   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3311)
  covalent geometry    : angle       0.53034 ( 4532)
  hydrogen bonds       : bond        0.03163 (  195)
  hydrogen bonds       : angle       4.21464 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.114 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
  outliers start: 13
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0292
  time to fit residues: 3.7451
Evaluate side-chains
  88 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7502

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.202620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.184289 restraints weight = 4631.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.186841 restraints weight = 3339.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.188517 restraints weight = 2629.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.189899 restraints weight = 2199.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.190891 restraints weight = 1925.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3311  Z= 0.118
  Angle     :  0.536   5.460   4532  Z= 0.283
  Chirality :  0.041   0.123    535
  Planarity :  0.004   0.044    558
  Dihedral  :  4.073  19.009    479
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.34 %
    Favored  : 66.12 %
  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 are not related in a simple way.
  whole: -0.46 (0.42), residues: 453
  helix:  1.06 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.22 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 278 
 PHE   0.012   0.001   PHE A 606 
 TRP   0.010   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3311)
  covalent geometry    : angle       0.53606 ( 4532)
  hydrogen bonds       : bond        0.03244 (  195)
  hydrogen bonds       : angle       4.24153 (  582)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.146 
Fit side-chains
Corrupt residue: chain: A residue: PRO 436 >>> skipping
  outliers start: 12
  outliers final: 12
  residues processed: 84
  average time/residue: 0.0192
  time to fit residues: 2.5118
Evaluate side-chains
  89 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  436 PRO
Chi-restraints excluded: chain A residue  443 TRP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0010
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.205304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.187139 restraints weight = 4707.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.189685 restraints weight = 3341.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.191665 restraints weight = 2604.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.192735 restraints weight = 2169.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.193998 restraints weight = 1902.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3311  Z= 0.103
  Angle     :  0.516   5.424   4532  Z= 0.271
  Chirality :  0.041   0.120    535
  Planarity :  0.004   0.043    558
  Dihedral  :  3.929  18.416    479
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 30.17 %
    Favored  : 65.29 %
  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 are not related in a simple way.
  whole: -0.29 (0.42), residues: 453
  helix:  1.23 (0.32), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.23 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.007   0.001   TYR A 278 
 PHE   0.007   0.001   PHE A 606 
 TRP   0.011   0.001   TRP A 720 
 HIS   0.000   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3311)
  covalent geometry    : angle       0.51624 ( 4532)
  hydrogen bonds       : bond        0.02884 (  195)
  hydrogen bonds       : angle       4.06753 (  582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 711.22 seconds
wall clock time: 12 minutes 54.11 seconds (774.11 seconds total)