Starting phenix.real_space_refine
on Tue Feb  3 14:27:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j73_61192/02_2026/9j73_61192.map"
  }
  resolution = 3.5
  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=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     S      25      5.16       5
     C    2382      2.51       5
     N     625      2.21       5
     O     618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 3652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3630
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 24, 'TRANS': 447}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'R75': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.96, per 1000 atoms: 0.26
  Number of scatterers: 3652
  At special positions: 0
  Unit cell: (90.1, 84.15, 73.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      2     34.99
     S      25     16.00
     O     618      8.00
     N     625      7.00
     C    2382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 139 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 137.6 milliseconds
  

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  868

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 2 sheets defined
      70.3% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.570A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 34
      removed outlier: 3.796A  pdb=" N   ALA A  21 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      Proline residue:  A  27  - end of helix
      removed outlier: 3.966A  pdb=" N   TRP A  30 " --> pdb=" O   THR A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 130 through 136
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 3.514A  pdb=" N   VAL A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 166
      No H-bonds generated for 'chain 'A' and resid 164 through 166'
    Processing helix  chain 'A' and resid 172 through 191
      removed outlier: 3.996A  pdb=" N   LEU A 176 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 225
      removed outlier: 3.511A  pdb=" N   TYR A 199 " --> pdb=" O   THR A 195 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   THR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 255
      removed outlier: 4.363A  pdb=" N   LEU A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   MET A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 238 " --> pdb=" O   MET A 234 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 276
      removed outlier: 3.553A  pdb=" N   GLN A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 263 " --> pdb=" O   ARG A 259 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 264 " --> pdb=" O   MET A 260 " (cutoff:3.500A)
      Proline residue:  A 268  - end of helix
      removed outlier: 3.989A  pdb=" N   LEU A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 3.816A  pdb=" N   LEU A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 289 " --> pdb=" O   TRP A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 307
    Processing helix  chain 'A' and resid 311 through 315
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 348 through 368
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 4.320A  pdb=" N   ARG A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 426
      removed outlier: 4.015A  pdb=" N   LEU A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      Proline residue:  A 416  - end of helix
      removed outlier: 3.559A  pdb=" N   ASN A 423 " --> pdb=" O   CYS A 419 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A 424 " --> pdb=" O   ILE A 420 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 455
      removed outlier: 3.943A  pdb=" N   LEU A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ALA A 438 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL A 439 " --> pdb=" O   SER A 435 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE A 449 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   THR A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 455 " --> pdb=" O   CYS A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 477
      removed outlier: 4.097A  pdb=" N   GLY A 470 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 491
      removed outlier: 4.499A  pdb=" N   VAL A 491 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 512
      removed outlier: 4.629A  pdb=" N   LEU A 498 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      Proline residue:  A 505  - end of helix
    Processing helix  chain 'A' and resid 513 through 515
      No H-bonds generated for 'chain 'A' and resid 513 through 515'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    193 hydrogen bonds defined for protein.
    561 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: 0.50

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1151
        1.34 -     1.48: 954
        1.48 -     1.62: 1591
        1.62 -     1.76: 0
        1.76 -     1.90: 42
  Bond restraints: 3738
  Sorted by residual:
  bond pdb=" CA  ALA A 368 "
       pdb=" CB  ALA A 368 "
    ideal  model  delta    sigma   weight residual
    1.536  1.485  0.051 1.53e-02 4.27e+03 1.09e+01
  bond pdb=" N   VAL A 251 "
       pdb=" CA  VAL A 251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" N   VAL A 452 "
       pdb=" CA  VAL A 452 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.00e+01
  bond pdb=" N   LEU A 247 "
       pdb=" CA  LEU A 247 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.23e-02 6.61e+03 9.49e+00
  bond pdb=" CA  SER A 242 "
       pdb=" CB  SER A 242 "
    ideal  model  delta    sigma   weight residual
    1.530  1.482  0.048 1.57e-02 4.06e+03 9.24e+00
  ... (remaining 3733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 4772
        1.81 -     3.63: 241
        3.63 -     5.44: 58
        5.44 -     7.25: 18
        7.25 -     9.07: 4
  Bond angle restraints: 5093
  Sorted by residual:
  angle pdb=" N   ALA A 480 "
        pdb=" CA  ALA A 480 "
        pdb=" C   ALA A 480 "
      ideal   model   delta    sigma   weight residual
     112.90  104.51    8.39 1.31e+00 5.83e-01 4.10e+01
  angle pdb=" N   LEU A 442 "
        pdb=" CA  LEU A 442 "
        pdb=" C   LEU A 442 "
      ideal   model   delta    sigma   weight residual
     111.71  104.72    6.99 1.15e+00 7.56e-01 3.69e+01
  angle pdb=" N   LEU A 384 "
        pdb=" CA  LEU A 384 "
        pdb=" C   LEU A 384 "
      ideal   model   delta    sigma   weight residual
     113.89  104.82    9.07 1.58e+00 4.01e-01 3.29e+01
  angle pdb=" CA  PHE A 362 "
        pdb=" CB  PHE A 362 "
        pdb=" CG  PHE A 362 "
      ideal   model   delta    sigma   weight residual
     113.80  119.51   -5.71 1.00e+00 1.00e+00 3.26e+01
  angle pdb=" N   ILE A 385 "
        pdb=" CA  ILE A 385 "
        pdb=" C   ILE A 385 "
      ideal   model   delta    sigma   weight residual
     112.98  106.01    6.97 1.25e+00 6.40e-01 3.11e+01
  ... (remaining 5088 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.94: 1854
       18.94 -    37.88: 256
       37.88 -    56.82: 60
       56.82 -    75.76: 16
       75.76 -    94.69: 3
  Dihedral angle restraints: 2189
    sinusoidal: 846
      harmonic: 1343
  Sorted by residual:
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 116 "
           pdb=" CB  CYS A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.46   70.46     1      1.00e+01 1.00e-02 6.39e+01
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 139 "
           pdb=" CB  CYS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.99  -67.99     1      1.00e+01 1.00e-02 6.00e+01
  dihedral pdb=" C   VAL A 452 "
           pdb=" N   VAL A 452 "
           pdb=" CA  VAL A 452 "
           pdb=" CB  VAL A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.59    9.59     0      2.50e+00 1.60e-01 1.47e+01
  ... (remaining 2186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 484
       0.060 -    0.119: 90
       0.119 -    0.178: 18
       0.178 -    0.238: 6
       0.238 -    0.297: 1
  Chirality restraints: 599
  Sorted by residual:
  chirality pdb=" CB  VAL A 452 "
            pdb=" CA  VAL A 452 "
            pdb=" CG1 VAL A 452 "
            pdb=" CG2 VAL A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  ILE A 385 "
            pdb=" N   ILE A 385 "
            pdb=" C   ILE A 385 "
            pdb=" CB  ILE A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  LEU A 367 "
            pdb=" N   LEU A 367 "
            pdb=" C   LEU A 367 "
            pdb=" CB  LEU A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 596 not shown)

  Planarity restraints: 631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAA R75 A 601 "   -0.058 2.00e-02 2.50e+03   5.39e-02 7.26e+01
        pdb=" CAB R75 A 601 "   -0.044 2.00e-02 2.50e+03
        pdb=" CAC R75 A 601 "   -0.031 2.00e-02 2.50e+03
        pdb=" CAD R75 A 601 "   -0.024 2.00e-02 2.50e+03
        pdb=" CAE R75 A 601 "   -0.037 2.00e-02 2.50e+03
        pdb=" CAF R75 A 601 "   -0.046 2.00e-02 2.50e+03
        pdb=" CAJ R75 A 601 "    0.097 2.00e-02 2.50e+03
        pdb=" OAG R75 A 601 "    0.008 2.00e-02 2.50e+03
        pdb="BR1  R75 A 601 "    0.058 2.00e-02 2.50e+03
        pdb="BR2  R75 A 601 "    0.076 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 441 "   -0.027 2.00e-02 2.50e+03   5.47e-02 3.00e+01
        pdb=" C   GLY A 441 "    0.095 2.00e-02 2.50e+03
        pdb=" O   GLY A 441 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   LEU A 442 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 230 "    0.063 5.00e-02 4.00e+02   9.32e-02 1.39e+01
        pdb=" N   PRO A 231 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO A 231 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 231 "    0.051 5.00e-02 4.00e+02
  ... (remaining 628 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 940
        2.79 -     3.32: 3480
        3.32 -     3.85: 5716
        3.85 -     4.37: 6299
        4.37 -     4.90: 11016
  Nonbonded interactions: 27451
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  72 "
            pdb=" OG  SER A  76 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ALA A  23 "
            pdb=" OH  TYR A 275 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OH  TYR A 122 "
            pdb=" OD1 ASP A 136 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   ALA A 252 "
            pdb=" N   GLY A 254 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   THR A 316 "
            pdb=" OG1 THR A 316 "
     model   vdw
     2.423 3.040
  ... (remaining 27446 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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.550
  Find NCS groups from input model:        0.010
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
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      :  0.006   0.095   3740  Z= 0.358
  Angle     :  0.994   9.067   5097  Z= 0.639
  Chirality :  0.053   0.297    599
  Planarity :  0.009   0.093    631
  Dihedral  : 18.217  94.694   1315
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.13 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 28.61 %
    Favored  : 67.78 %
  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: -1.64 (0.40), residues: 464
  helix: -0.42 (0.30), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.53 (0.51), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  90 
 TYR   0.012   0.001   TYR A 492 
 PHE   0.022   0.002   PHE A 362 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.001   0.000   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 3738)
  covalent geometry    : angle       0.99407 ( 5093)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.39970 (    4)
  hydrogen bonds       : bond        0.19116 (  193)
  hydrogen bonds       : angle       6.40459 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A    4 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8085 (Cg_endo)
REVERT: A  272 PHE cc_start: 0.7362 (m-80) cc_final: 0.6903 (m-80)
REVERT: A  411 SER cc_start: 0.8789 (t) cc_final: 0.8382 (p)
REVERT: A  415 LEU cc_start: 0.8454 (tm) cc_final: 0.8213 (tm)
  outliers start: 14
  outliers final: 3
  residues processed: 105
  average time/residue: 0.0577
  time to fit residues: 7.4260
Evaluate side-chains
  64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
A  17 GLN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.196122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.141340 restraints weight = 4495.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.145002 restraints weight = 2936.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.147376 restraints weight = 2302.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.148434 restraints weight = 2006.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.148623 restraints weight = 1866.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3740  Z= 0.139
  Angle     :  0.649   8.393   5097  Z= 0.316
  Chirality :  0.040   0.161    599
  Planarity :  0.006   0.053    631
  Dihedral  :  7.038  69.056    517
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 28.87 %
    Favored  : 66.75 %
  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: -1.04 (0.40), residues: 464
  helix:  0.03 (0.30), residues: 332
  sheet:  None (None), residues: 0
  loop : -2.42 (0.49), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 308 
 TYR   0.005   0.001   TYR A 253 
 PHE   0.017   0.001   PHE A 204 
 TRP   0.008   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3738)
  covalent geometry    : angle       0.64956 ( 5093)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.51719 (    4)
  hydrogen bonds       : bond        0.04324 (  193)
  hydrogen bonds       : angle       4.24714 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.6968 (mpp)
REVERT: A  222 MET cc_start: 0.7739 (tpp) cc_final: 0.7485 (mmt)
REVERT: A  272 PHE cc_start: 0.7758 (m-80) cc_final: 0.7192 (m-80)
REVERT: A  411 SER cc_start: 0.8921 (t) cc_final: 0.8599 (p)
  outliers start: 17
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0589
  time to fit residues: 5.8081
Evaluate side-chains
  63 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  414 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0570
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   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 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.197160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141914 restraints weight = 4176.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.145831 restraints weight = 2669.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148115 restraints weight = 2060.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.149734 restraints weight = 1775.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.150192 restraints weight = 1632.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3740  Z= 0.117
  Angle     :  0.579   6.789   5097  Z= 0.282
  Chirality :  0.038   0.128    599
  Planarity :  0.005   0.053    631
  Dihedral  :  5.932  66.004    514
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.55 %
    Favored  : 69.33 %
  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: -0.40 (0.40), residues: 464
  helix:  0.47 (0.30), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.05 (0.51), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  48 
 TYR   0.004   0.001   TYR A 275 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.007   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3738)
  covalent geometry    : angle       0.57878 ( 5093)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.18091 (    4)
  hydrogen bonds       : bond        0.03805 (  193)
  hydrogen bonds       : angle       3.94673 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.6836 (mpp)
REVERT: A  260 MET cc_start: 0.7677 (mmp) cc_final: 0.7404 (mmp)
REVERT: A  272 PHE cc_start: 0.7675 (m-80) cc_final: 0.7064 (m-80)
REVERT: A  351 PHE cc_start: 0.7704 (t80) cc_final: 0.7480 (t80)
REVERT: A  411 SER cc_start: 0.8922 (t) cc_final: 0.8674 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0619
  time to fit residues: 5.5183
Evaluate side-chains
  70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0570
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   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 306 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.193179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.137481 restraints weight = 4253.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141398 restraints weight = 2700.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143705 restraints weight = 2066.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145384 restraints weight = 1775.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.145972 restraints weight = 1624.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3740  Z= 0.117
  Angle     :  0.561   7.957   5097  Z= 0.273
  Chirality :  0.038   0.125    599
  Planarity :  0.005   0.053    631
  Dihedral  :  5.763  66.540    514
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 27.32 %
    Favored  : 69.07 %
  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: -0.11 (0.41), residues: 464
  helix:  0.70 (0.30), residues: 334
  sheet:  None (None), residues: 0
  loop : -2.03 (0.53), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  48 
 TYR   0.006   0.001   TYR A 275 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.007   0.001   TRP A 258 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3738)
  covalent geometry    : angle       0.56137 ( 5093)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.12539 (    4)
  hydrogen bonds       : bond        0.03631 (  193)
  hydrogen bonds       : angle       3.86076 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.6965 (mpp)
REVERT: A  222 MET cc_start: 0.7691 (tpp) cc_final: 0.7460 (mmt)
REVERT: A  234 MET cc_start: 0.7701 (mmm) cc_final: 0.7244 (mmp)
REVERT: A  272 PHE cc_start: 0.7664 (m-80) cc_final: 0.7057 (m-80)
REVERT: A  411 SER cc_start: 0.8838 (t) cc_final: 0.8555 (p)
REVERT: A  419 CYS cc_start: 0.7068 (m) cc_final: 0.6834 (m)
REVERT: A  430 MET cc_start: 0.6672 (mpp) cc_final: 0.6074 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0374
  time to fit residues: 3.3425
Evaluate side-chains
  67 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   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 228 GLN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.194406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135995 restraints weight = 4323.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.140071 restraints weight = 2724.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142597 restraints weight = 2096.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143701 restraints weight = 1812.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143705 restraints weight = 1682.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3740  Z= 0.124
  Angle     :  0.565   7.451   5097  Z= 0.274
  Chirality :  0.039   0.129    599
  Planarity :  0.005   0.053    631
  Dihedral  :  5.704  65.900    514
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 27.84 %
    Favored  : 68.56 %
  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: -0.11 (0.41), residues: 464
  helix:  0.73 (0.31), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.02 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 321 
 TYR   0.005   0.001   TYR A 275 
 PHE   0.017   0.002   PHE A 351 
 TRP   0.007   0.001   TRP A 258 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3738)
  covalent geometry    : angle       0.56502 ( 5093)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.12956 (    4)
  hydrogen bonds       : bond        0.03739 (  193)
  hydrogen bonds       : angle       3.81684 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7064 (mpp)
REVERT: A  272 PHE cc_start: 0.7724 (m-80) cc_final: 0.7112 (m-80)
REVERT: A  393 LYS cc_start: 0.6936 (ptmm) cc_final: 0.6478 (ptpp)
REVERT: A  411 SER cc_start: 0.8631 (t) cc_final: 0.8333 (p)
REVERT: A  419 CYS cc_start: 0.7196 (m) cc_final: 0.6955 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0442
  time to fit residues: 3.7134
Evaluate side-chains
  67 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 228 GLN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.194141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.136901 restraints weight = 4246.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140911 restraints weight = 2662.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.143566 restraints weight = 2031.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.144790 restraints weight = 1751.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.146084 restraints weight = 1614.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3740  Z= 0.108
  Angle     :  0.548   7.969   5097  Z= 0.265
  Chirality :  0.038   0.122    599
  Planarity :  0.005   0.055    631
  Dihedral  :  5.564  63.792    514
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 28.61 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.05 (0.41), residues: 464
  helix:  0.86 (0.31), residues: 331
  sheet:  None (None), residues: 0
  loop : -2.04 (0.51), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 434 
 TYR   0.004   0.001   TYR A 275 
 PHE   0.017   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 258 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3738)
  covalent geometry    : angle       0.54866 ( 5093)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.07375 (    4)
  hydrogen bonds       : bond        0.03395 (  193)
  hydrogen bonds       : angle       3.71991 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.6992 (mpp)
REVERT: A  272 PHE cc_start: 0.7680 (m-80) cc_final: 0.7063 (m-80)
REVERT: A  411 SER cc_start: 0.8584 (t) cc_final: 0.8305 (p)
REVERT: A  419 CYS cc_start: 0.7132 (m) cc_final: 0.6905 (m)
REVERT: A  430 MET cc_start: 0.6740 (mpp) cc_final: 0.6043 (mpp)
  outliers start: 13
  outliers final: 8
  residues processed: 61
  average time/residue: 0.0450
  time to fit residues: 3.5788
Evaluate side-chains
  60 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0000
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.193011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135481 restraints weight = 4334.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.139486 restraints weight = 2702.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.142203 restraints weight = 2064.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.143382 restraints weight = 1769.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.144617 restraints weight = 1634.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3740  Z= 0.115
  Angle     :  0.561   7.776   5097  Z= 0.270
  Chirality :  0.038   0.125    599
  Planarity :  0.005   0.055    631
  Dihedral  :  5.566  63.266    514
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 28.09 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.16 (0.41), residues: 464
  helix:  1.02 (0.31), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.11 (0.49), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 434 
 TYR   0.005   0.001   TYR A 275 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.008   0.001   TRP A 258 
 HIS   0.001   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3738)
  covalent geometry    : angle       0.56092 ( 5093)
  SS BOND              : bond        0.00097 (    2)
  SS BOND              : angle       0.11377 (    4)
  hydrogen bonds       : bond        0.03511 (  193)
  hydrogen bonds       : angle       3.67727 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.6988 (mpp)
REVERT: A  222 MET cc_start: 0.7787 (tpp) cc_final: 0.7572 (mmt)
REVERT: A  272 PHE cc_start: 0.7703 (m-80) cc_final: 0.7091 (m-80)
REVERT: A  411 SER cc_start: 0.8525 (t) cc_final: 0.8237 (p)
REVERT: A  419 CYS cc_start: 0.7188 (m) cc_final: 0.6970 (m)
REVERT: A  430 MET cc_start: 0.6710 (mpp) cc_final: 0.6508 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 65
  average time/residue: 0.0648
  time to fit residues: 5.3294
Evaluate side-chains
  64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0570
   chunk 25 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.4122 r_free = 0.4122 target = 0.194773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.137214 restraints weight = 4282.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.141289 restraints weight = 2683.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.143943 restraints weight = 2051.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.145026 restraints weight = 1760.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.146247 restraints weight = 1631.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3740  Z= 0.107
  Angle     :  0.574   7.942   5097  Z= 0.270
  Chirality :  0.038   0.155    599
  Planarity :  0.005   0.055    631
  Dihedral  :  5.447  61.244    514
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 28.09 %
    Favored  : 69.07 %
  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:  0.22 (0.41), residues: 464
  helix:  0.98 (0.31), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.98 (0.51), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.004   0.001   TYR A 199 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.008   0.001   TRP A 258 
 HIS   0.000   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3738)
  covalent geometry    : angle       0.57431 ( 5093)
  SS BOND              : bond        0.00082 (    2)
  SS BOND              : angle       0.12618 (    4)
  hydrogen bonds       : bond        0.03182 (  193)
  hydrogen bonds       : angle       3.59816 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.6918 (mpp)
REVERT: A  272 PHE cc_start: 0.7615 (m-80) cc_final: 0.6990 (m-80)
REVERT: A  411 SER cc_start: 0.8521 (t) cc_final: 0.8234 (p)
REVERT: A  419 CYS cc_start: 0.7200 (m) cc_final: 0.6996 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0633
  time to fit residues: 5.0953
Evaluate side-chains
  64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0170
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 42 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0020
   overall best weight:    0.3626

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.196931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.139126 restraints weight = 4265.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143174 restraints weight = 2661.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.145922 restraints weight = 2032.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.147547 restraints weight = 1738.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.147547 restraints weight = 1594.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3740  Z= 0.105
  Angle     :  0.566   7.860   5097  Z= 0.268
  Chirality :  0.038   0.126    599
  Planarity :  0.005   0.054    631
  Dihedral  :  5.225  59.243    514
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 28.35 %
    Favored  : 68.81 %
  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:  0.33 (0.41), residues: 464
  helix:  1.04 (0.31), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.87 (0.52), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.004   0.001   TYR A 275 
 PHE   0.018   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 258 
 HIS   0.000   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3738)
  covalent geometry    : angle       0.56635 ( 5093)
  SS BOND              : bond        0.00069 (    2)
  SS BOND              : angle       0.23461 (    4)
  hydrogen bonds       : bond        0.03143 (  193)
  hydrogen bonds       : angle       3.55961 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.6858 (mpp)
REVERT: A  272 PHE cc_start: 0.7643 (m-80) cc_final: 0.7001 (m-80)
REVERT: A  411 SER cc_start: 0.8513 (t) cc_final: 0.8233 (p)
REVERT: A  419 CYS cc_start: 0.7216 (m) cc_final: 0.7009 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0741
  time to fit residues: 5.8057
Evaluate side-chains
  65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.193491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.135880 restraints weight = 4277.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.139877 restraints weight = 2678.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.142464 restraints weight = 2049.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143507 restraints weight = 1762.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144664 restraints weight = 1635.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3740  Z= 0.115
  Angle     :  0.581   7.831   5097  Z= 0.275
  Chirality :  0.039   0.122    599
  Planarity :  0.005   0.055    631
  Dihedral  :  5.226  60.351    514
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 28.61 %
    Favored  : 69.07 %
  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 (0.41), residues: 464
  helix:  1.00 (0.31), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.84 (0.52), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.005   0.001   TYR A 275 
 PHE   0.019   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 258 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3738)
  covalent geometry    : angle       0.58098 ( 5093)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       0.22168 (    4)
  hydrogen bonds       : bond        0.03405 (  193)
  hydrogen bonds       : angle       3.59762 (  561)

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

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

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  928 Ramachandran restraints generated.
    464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.6915 (mpp)
REVERT: A  272 PHE cc_start: 0.7708 (m-80) cc_final: 0.7072 (m-80)
REVERT: A  419 CYS cc_start: 0.7391 (m) cc_final: 0.7187 (m)
REVERT: A  430 MET cc_start: 0.6734 (mpp) cc_final: 0.6408 (mmm)
  outliers start: 9
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0749
  time to fit residues: 5.5485
Evaluate side-chains
  62 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  275 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  388 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0170
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 6 optimal weight:    0.0170
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.2654

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.196245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.139247 restraints weight = 4199.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143248 restraints weight = 2633.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.145962 restraints weight = 2012.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.147200 restraints weight = 1727.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.148184 restraints weight = 1588.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3740  Z= 0.105
  Angle     :  0.569   7.828   5097  Z= 0.270
  Chirality :  0.038   0.126    599
  Planarity :  0.005   0.054    631
  Dihedral  :  4.911  58.082    514
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 28.61 %
    Favored  : 69.07 %
  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:  0.43 (0.42), residues: 464
  helix:  1.08 (0.31), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.74 (0.53), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.004   0.001   TYR A 199 
 PHE   0.016   0.001   PHE A 204 
 TRP   0.009   0.001   TRP A 258 
 HIS   0.000   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3738)
  covalent geometry    : angle       0.56957 ( 5093)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.23367 (    4)
  hydrogen bonds       : bond        0.03006 (  193)
  hydrogen bonds       : angle       3.52166 (  561)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 835.35 seconds
wall clock time: 14 minutes 58.27 seconds (898.27 seconds total)