Starting phenix.real_space_refine
on Sun Apr 27 05:15:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q3f_18126/04_2025/8q3f_18126.cif"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.009
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      41      5.16       5
     C    2903      2.51       5
     N     776      2.21       5
     O     879      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4599
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4599
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 24, 'TRANS': 553}
  Time building chain proxies: 3.46, per 1000 atoms: 0.75
  Number of scatterers: 4599
  At special positions: 0
  Unit cell: (67.08, 97.18, 104.06, 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      41     16.00
     O     879      8.00
     N     776      7.00
     C    2903      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 124 " - pdb=" SG  CYS A 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 168 " - pdb=" SG  CYS A 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 246 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 265 " - pdb=" SG  CYS A 279 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 316 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 360 " - pdb=" SG  CYS A 369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 392 " - pdb=" SG  CYS A 438 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 437 " - pdb=" SG  CYS A 448 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 461 " - pdb=" SG  CYS A 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 487 " 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: 1.18
  Conformation dependent library (CDL) restraints added in 588.2 milliseconds
  

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1134

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      70.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 31
      removed outlier: 3.654A  pdb=" N   LYS A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 54
      removed outlier: 3.701A  pdb=" N   VAL A  40 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LYS A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 78
      removed outlier: 3.787A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   CYS A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   THR A  76 " --> pdb=" O   ASP A  72 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.300A  pdb=" N   MET A  87 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 103
    Processing helix  chain 'A' and resid 119 through 130
      removed outlier: 4.377A  pdb=" N   MET A 123 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 143
    Processing helix  chain 'A' and resid 150 through 152
      No H-bonds generated for 'chain 'A' and resid 150 through 152'
    Processing helix  chain 'A' and resid 153 through 166
    Processing helix  chain 'A' and resid 174 through 206
      removed outlier: 4.057A  pdb=" N   LEU A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      Proline residue:  A 180  - end of helix
    Processing helix  chain 'A' and resid 208 through 223
    Processing helix  chain 'A' and resid 227 through 244
      removed outlier: 3.789A  pdb=" N   VAL A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 267
    Processing helix  chain 'A' and resid 282 through 291
      removed outlier: 3.833A  pdb=" N   ILE A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   ALA A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 3.656A  pdb=" N   PHE A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 322
    Processing helix  chain 'A' and resid 323 through 336
    Processing helix  chain 'A' and resid 342 through 361
      removed outlier: 3.855A  pdb=" N   LYS A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 399
      removed outlier: 3.976A  pdb=" N   LEU A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU A 383 " --> pdb=" O   PRO A 379 " (cutoff:3.500A)
      Proline residue:  A 384  - end of helix
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.548A  pdb=" N   TYR A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 437
      removed outlier: 3.702A  pdb=" N   LEU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   CYS A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 452 through 467
      removed outlier: 3.935A  pdb=" N   VAL A 456 " --> pdb=" O   TYR A 452 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN A 458 " --> pdb=" O   SER A 454 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LYS A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR A 467 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 478
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 4.300A  pdb=" N   CYS A 514 " --> pdb=" O   ALA A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 536
    Processing helix  chain 'A' and resid 540 through 561
      removed outlier: 3.586A  pdb=" N   LYS A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ALA A 546 " --> pdb=" O   GLU A 542 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   CYS A 558 " --> pdb=" O   PHE A 554 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS A 560 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 578
      removed outlier: 3.593A  pdb=" N   LYS A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    741 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: 1.13

  Time building geometry restraints manager: 1.45 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: 1145
        1.33 -     1.46: 1038
        1.46 -     1.58: 2458
        1.58 -     1.71: 0
        1.71 -     1.83: 47
  Bond restraints: 4688
  Sorted by residual:
  bond pdb=" C   GLU A  95 "
       pdb=" N   PRO A  96 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 8.06e+00
  bond pdb=" C   THR A 420 "
       pdb=" N   PRO A 421 "
    ideal  model  delta    sigma   weight residual
    1.337  1.367 -0.030 1.24e-02 6.50e+03 5.91e+00
  bond pdb=" C   GLU A 383 "
       pdb=" N   PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.337  1.365 -0.028 1.24e-02 6.50e+03 5.20e+00
  bond pdb=" C   LEU A 179 "
       pdb=" N   PRO A 180 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.25e-02 6.40e+03 3.12e+00
  bond pdb=" C   MET A 446 "
       pdb=" N   PRO A 447 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.021 1.23e-02 6.61e+03 2.86e+00
  ... (remaining 4683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 6058
        2.36 -     4.72: 204
        4.72 -     7.08: 41
        7.08 -     9.44: 13
        9.44 -    11.80: 8
  Bond angle restraints: 6324
  Sorted by residual:
  angle pdb=" C   GLU A  95 "
        pdb=" N   PRO A  96 "
        pdb=" CA  PRO A  96 "
      ideal   model   delta    sigma   weight residual
     120.96  114.15    6.81 1.41e+00 5.03e-01 2.33e+01
  angle pdb=" CG1 VAL A 415 "
        pdb=" CB  VAL A 415 "
        pdb=" CG2 VAL A 415 "
      ideal   model   delta    sigma   weight residual
     110.80  101.30    9.50 2.20e+00 2.07e-01 1.86e+01
  angle pdb=" N   GLN A 526 "
        pdb=" CA  GLN A 526 "
        pdb=" CB  GLN A 526 "
      ideal   model   delta    sigma   weight residual
     110.40  116.91   -6.51 1.63e+00 3.76e-01 1.59e+01
  angle pdb=" CA  PRO A 384 "
        pdb=" N   PRO A 384 "
        pdb=" CD  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     112.00  106.58    5.42 1.40e+00 5.10e-01 1.50e+01
  angle pdb=" CA  PRO A 421 "
        pdb=" N   PRO A 421 "
        pdb=" CD  PRO A 421 "
      ideal   model   delta    sigma   weight residual
     112.00  106.70    5.30 1.40e+00 5.10e-01 1.44e+01
  ... (remaining 6319 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 2582
       17.61 -    35.21: 306
       35.21 -    52.82: 48
       52.82 -    70.43: 6
       70.43 -    88.03: 10
  Dihedral angle restraints: 2952
    sinusoidal: 1223
      harmonic: 1729
  Sorted by residual:
  dihedral pdb=" CB  CYS A 124 "
           pdb=" SG  CYS A 124 "
           pdb=" SG  CYS A 169 "
           pdb=" CB  CYS A 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.01  -81.01     1      1.00e+01 1.00e-02 8.10e+01
  dihedral pdb=" CB  CYS A 461 "
           pdb=" SG  CYS A 461 "
           pdb=" SG  CYS A 477 "
           pdb=" CB  CYS A 477 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.04  -77.04     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS A 392 "
           pdb=" SG  CYS A 392 "
           pdb=" SG  CYS A 438 "
           pdb=" CB  CYS A 438 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.69   73.69     1      1.00e+01 1.00e-02 6.90e+01
  ... (remaining 2949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 553
       0.067 -    0.134: 115
       0.134 -    0.201: 22
       0.201 -    0.268: 10
       0.268 -    0.335: 3
  Chirality restraints: 703
  Sorted by residual:
  chirality pdb=" CB  VAL A 418 "
            pdb=" CA  VAL A 418 "
            pdb=" CG1 VAL A 418 "
            pdb=" CG2 VAL A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CG  LEU A 154 "
            pdb=" CB  LEU A 154 "
            pdb=" CD1 LEU A 154 "
            pdb=" CD2 LEU A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  VAL A 381 "
            pdb=" CA  VAL A 381 "
            pdb=" CG1 VAL A 381 "
            pdb=" CG2 VAL A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 700 not shown)

  Planarity restraints: 824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 151 "    0.050 5.00e-02 4.00e+02   7.36e-02 8.68e+00
        pdb=" N   PRO A 152 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 152 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 152 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 281 "    0.046 5.00e-02 4.00e+02   7.03e-02 7.91e+00
        pdb=" N   PRO A 282 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  34 "    0.042 5.00e-02 4.00e+02   6.25e-02 6.25e+00
        pdb=" N   PRO A  35 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A  35 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  35 "    0.035 5.00e-02 4.00e+02
  ... (remaining 821 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1525
        2.85 -     3.36: 4096
        3.36 -     3.88: 7405
        3.88 -     4.39: 7696
        4.39 -     4.90: 13195
  Nonbonded interactions: 33917
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 235 "
            pdb=" OG1 THR A 239 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   ALA A 226 "
            pdb=" OH  TYR A 332 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   SER A   5 "
            pdb=" OG  SER A   5 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" O   SER A 232 "
            pdb=" OG1 THR A 236 "
     model   vdw
     2.404 3.040
  nonbonded pdb=" O   CYS A 514 "
            pdb=" NH2 ARG A 521 "
     model   vdw
     2.425 3.120
  ... (remaining 33912 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=0.00 max=1.00 mean=0.87
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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.910
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   4701  Z= 0.264
  Angle     :  1.122  11.803   6350  Z= 0.577
  Chirality :  0.065   0.335    703
  Planarity :  0.008   0.074    824
  Dihedral  : 15.048  88.031   1779
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.05 (0.22), residues: 576
  helix: -3.30 (0.16), residues: 400
  sheet:  None (None), residues: 0
  loop : -2.91 (0.33), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 214 
 HIS   0.005   0.001   HIS A  39 
 PHE   0.042   0.002   PHE A 149 
 TYR   0.025   0.002   TYR A 411 
 ARG   0.004   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16452 (  251)
  hydrogen bonds       : angle       6.57720 (  741)
  SS BOND              : bond        0.00251 (   13)
  SS BOND              : angle       1.81918 (   26)
  covalent geometry    : bond        0.00545 ( 4688)
  covalent geometry    : angle       1.11804 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  8 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8679 (mmp) cc_final: 0.8461 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1372
  time to fit residues: 2.2505
Evaluate side-chains
  6 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 6
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.052775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.042870 restraints weight = 34063.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044125 restraints weight = 17948.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.045003 restraints weight = 11886.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      609 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4701  Z= 0.095
  Angle     :  0.514   6.165   6350  Z= 0.269
  Chirality :  0.037   0.129    703
  Planarity :  0.004   0.042    824
  Dihedral  :  4.375  20.719    619
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.32), residues: 576
  helix: -0.64 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -2.18 (0.38), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.025   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.003   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03215 (  251)
  hydrogen bonds       : angle       3.91579 (  741)
  SS BOND              : bond        0.00223 (   13)
  SS BOND              : angle       0.97511 (   26)
  covalent geometry    : bond        0.00201 ( 4688)
  covalent geometry    : angle       0.51166 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8677 (mmp) cc_final: 0.8462 (mmm)
REVERT: A  123 MET cc_start: 0.8893 (pmm) cc_final: 0.8659 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1449
  time to fit residues: 2.7310
Evaluate side-chains
  6 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 6
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 36 optimal weight:    0.0000
   chunk 51 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.053106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.043127 restraints weight = 35018.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044392 restraints weight = 18334.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.045281 restraints weight = 12220.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4701  Z= 0.085
  Angle     :  0.485   7.782   6350  Z= 0.247
  Chirality :  0.037   0.127    703
  Planarity :  0.003   0.037    824
  Dihedral  :  3.872  17.225    619
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  9.68 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.35), residues: 576
  helix:  0.49 (0.27), residues: 389
  sheet:  None (None), residues: 0
  loop : -1.84 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.024   0.001   PHE A 554 
 TYR   0.009   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02706 (  251)
  hydrogen bonds       : angle       3.50936 (  741)
  SS BOND              : bond        0.00190 (   13)
  SS BOND              : angle       0.68218 (   26)
  covalent geometry    : bond        0.00176 ( 4688)
  covalent geometry    : angle       0.48417 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 8
  time to evaluate  : 0.594 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8813 (mmp) cc_final: 0.8612 (mmm)
REVERT: A  123 MET cc_start: 0.8837 (pmm) cc_final: 0.8425 (pmm)
REVERT: A  446 MET cc_start: 0.7181 (mmm) cc_final: 0.6894 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1486
  time to fit residues: 2.5184
Evaluate side-chains
  7 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0060
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.6002

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.051737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.041582 restraints weight = 34786.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.042797 restraints weight = 18364.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.043617 restraints weight = 12330.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4701  Z= 0.118
  Angle     :  0.500   6.422   6350  Z= 0.257
  Chirality :  0.037   0.127    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.785  16.125    619
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.26 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.37), residues: 576
  helix:  0.89 (0.28), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.61 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 464 
 PHE   0.035   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03135 (  251)
  hydrogen bonds       : angle       3.43703 (  741)
  SS BOND              : bond        0.00176 (   13)
  SS BOND              : angle       0.68260 (   26)
  covalent geometry    : bond        0.00258 ( 4688)
  covalent geometry    : angle       0.49866 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 8
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8956 (mmp) cc_final: 0.8577 (tpp)
REVERT: A  123 MET cc_start: 0.9050 (pmm) cc_final: 0.8784 (pmm)
  outliers start: 3
  outliers final: 1
  residues processed: 11
  average time/residue: 0.1336
  time to fit residues: 2.8082
Evaluate side-chains
  7 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 6
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.052473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.042361 restraints weight = 35119.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.043644 restraints weight = 18245.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.044474 restraints weight = 12124.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4701  Z= 0.088
  Angle     :  0.464   6.264   6350  Z= 0.240
  Chirality :  0.037   0.131    703
  Planarity :  0.003   0.033    824
  Dihedral  :  3.648  14.299    619
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 11.86 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.37), residues: 576
  helix:  1.29 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.40 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.038   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02633 (  251)
  hydrogen bonds       : angle       3.30083 (  741)
  SS BOND              : bond        0.00160 (   13)
  SS BOND              : angle       0.54914 (   26)
  covalent geometry    : bond        0.00186 ( 4688)
  covalent geometry    : angle       0.46368 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 9
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9020 (mmp) cc_final: 0.8637 (tpp)
REVERT: A  123 MET cc_start: 0.9097 (pmm) cc_final: 0.8645 (pmm)
  outliers start: 2
  outliers final: 2
  residues processed: 11
  average time/residue: 0.1410
  time to fit residues: 2.9169
Evaluate side-chains
  8 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 6
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.051096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.040792 restraints weight = 34443.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.041989 restraints weight = 18257.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.042782 restraints weight = 12333.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4701  Z= 0.162
  Angle     :  0.541   6.458   6350  Z= 0.280
  Chirality :  0.039   0.128    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.796  14.989    619
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.65 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.37), residues: 576
  helix:  1.21 (0.28), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.48 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 214 
 HIS   0.004   0.001   HIS A 464 
 PHE   0.014   0.001   PHE A 149 
 TYR   0.012   0.001   TYR A 370 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  251)
  hydrogen bonds       : angle       3.48012 (  741)
  SS BOND              : bond        0.00183 (   13)
  SS BOND              : angle       0.65353 (   26)
  covalent geometry    : bond        0.00359 ( 4688)
  covalent geometry    : angle       0.54007 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 8
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9093 (mmp) cc_final: 0.8745 (tpp)
REVERT: A  123 MET cc_start: 0.9113 (pmm) cc_final: 0.8628 (pmm)
  outliers start: 4
  outliers final: 3
  residues processed: 12
  average time/residue: 0.1382
  time to fit residues: 3.1253
Evaluate side-chains
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 7
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0970
   chunk 49 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.4182

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.051604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.041415 restraints weight = 34247.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.042645 restraints weight = 18109.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.043452 restraints weight = 12143.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4701  Z= 0.106
  Angle     :  0.487   6.428   6350  Z= 0.250
  Chirality :  0.038   0.127    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.749  13.740    619
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.04 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.37), residues: 576
  helix:  1.48 (0.28), residues: 400
  sheet:  None (None), residues: 0
  loop : -1.37 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 
 PHE   0.033   0.001   PHE A 554 
 TYR   0.011   0.001   TYR A 370 
 ARG   0.002   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02808 (  251)
  hydrogen bonds       : angle       3.34079 (  741)
  SS BOND              : bond        0.00156 (   13)
  SS BOND              : angle       0.58472 (   26)
  covalent geometry    : bond        0.00235 ( 4688)
  covalent geometry    : angle       0.48675 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 8
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9101 (mmp) cc_final: 0.8749 (tpp)
REVERT: A  123 MET cc_start: 0.9121 (pmm) cc_final: 0.8618 (pmm)
  outliers start: 5
  outliers final: 3
  residues processed: 13
  average time/residue: 0.1180
  time to fit residues: 2.8825
Evaluate side-chains
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 8
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.051312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.041057 restraints weight = 34005.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.042245 restraints weight = 18021.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.043060 restraints weight = 12198.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4701  Z= 0.122
  Angle     :  0.511   7.546   6350  Z= 0.262
  Chirality :  0.039   0.131    703
  Planarity :  0.003   0.036    824
  Dihedral  :  3.748  14.089    619
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.64 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.37), residues: 576
  helix:  1.45 (0.28), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.39 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 464 
 PHE   0.015   0.001   PHE A 149 
 TYR   0.012   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03014 (  251)
  hydrogen bonds       : angle       3.37323 (  741)
  SS BOND              : bond        0.00167 (   13)
  SS BOND              : angle       0.58626 (   26)
  covalent geometry    : bond        0.00271 ( 4688)
  covalent geometry    : angle       0.51019 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 8
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9118 (mmp) cc_final: 0.8760 (tpp)
REVERT: A  123 MET cc_start: 0.9098 (pmm) cc_final: 0.8581 (pmm)
  outliers start: 5
  outliers final: 3
  residues processed: 13
  average time/residue: 0.1175
  time to fit residues: 2.8670
Evaluate side-chains
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 7
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.051542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.041189 restraints weight = 34381.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.042428 restraints weight = 18167.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043237 restraints weight = 12190.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4701  Z= 0.114
  Angle     :  0.513   7.441   6350  Z= 0.262
  Chirality :  0.039   0.215    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.756  16.452    619
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.43 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.37), residues: 576
  helix:  1.60 (0.28), residues: 399
  sheet:  None (None), residues: 0
  loop : -1.28 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 
 PHE   0.016   0.001   PHE A 554 
 TYR   0.012   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02893 (  251)
  hydrogen bonds       : angle       3.38302 (  741)
  SS BOND              : bond        0.00165 (   13)
  SS BOND              : angle       0.58964 (   26)
  covalent geometry    : bond        0.00253 ( 4688)
  covalent geometry    : angle       0.51316 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 7
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9126 (mmp) cc_final: 0.8775 (tpp)
REVERT: A  123 MET cc_start: 0.9097 (pmm) cc_final: 0.8637 (pmm)
  outliers start: 4
  outliers final: 4
  residues processed: 11
  average time/residue: 0.1196
  time to fit residues: 2.5846
Evaluate side-chains
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 7
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  438 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.052108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.041862 restraints weight = 34274.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.043110 restraints weight = 17979.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.043954 restraints weight = 12024.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4701  Z= 0.092
  Angle     :  0.487   6.816   6350  Z= 0.248
  Chirality :  0.039   0.228    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.602  13.249    619
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 14.23 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.37), residues: 576
  helix:  1.81 (0.28), residues: 394
  sheet:  None (None), residues: 0
  loop : -1.22 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 214 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.014   0.001   PHE A 554 
 TYR   0.011   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02546 (  251)
  hydrogen bonds       : angle       3.27610 (  741)
  SS BOND              : bond        0.00163 (   13)
  SS BOND              : angle       0.54719 (   26)
  covalent geometry    : bond        0.00200 ( 4688)
  covalent geometry    : angle       0.48714 ( 6324)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 7
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8633 (pmm)
  outliers start: 5
  outliers final: 4
  residues processed: 11
  average time/residue: 0.1317
  time to fit residues: 2.7672
Evaluate side-chains
  12 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 7
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  438 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  526 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.052237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.042000 restraints weight = 34395.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.043245 restraints weight = 18175.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.044069 restraints weight = 12193.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4701  Z= 0.090
  Angle     :  0.498   8.179   6350  Z= 0.249
  Chirality :  0.039   0.209    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.553  12.612    619
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 14.43 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.37), residues: 576
  helix:  1.85 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.17 (0.46), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 214 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.013   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02545 (  251)
  hydrogen bonds       : angle       3.22194 (  741)
  SS BOND              : bond        0.00163 (   13)
  SS BOND              : angle       0.53989 (   26)
  covalent geometry    : bond        0.00196 ( 4688)
  covalent geometry    : angle       0.49799 ( 6324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1743.76 seconds
wall clock time: 30 minutes 44.12 seconds (1844.12 seconds total)