Starting phenix.real_space_refine
on Fri Aug 22 15:04:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q3f_18126/08_2025/8q3f_18126.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q3f_18126/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q3f_18126/08_2025/8q3f_18126.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q3f_18126/08_2025/8q3f_18126.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q3f_18126/08_2025/8q3f_18126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q3f_18126/08_2025/8q3f_18126.map"
  }
  resolution = 3.77
  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=   0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.01, per 1000 atoms: 0.22
  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: 0.21
  Conformation dependent library (CDL) restraints added in 158.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.08
  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: 0.39

  Time building geometry restraints manager: 0.32 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:             1.040
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.540
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.490
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.004   0.000   ARG A  98 
 TYR   0.025   0.002   TYR A 411 
 PHE   0.042   0.002   PHE A 149 
 TRP   0.005   0.002   TRP A 214 
 HIS   0.005   0.001   HIS A  39 

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

*********************** 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  : 0.130 
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: 0.0376
  time to fit residues: 0.6023
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0270
   overall best weight:    0.8398

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.052740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.042818 restraints weight = 34366.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044102 restraints weight = 17995.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.044977 restraints weight = 11878.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.045412 restraints weight = 9060.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.045863 restraints weight = 7744.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      609 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4701  Z= 0.101
  Angle     :  0.527   6.290   6350  Z= 0.275
  Chirality :  0.038   0.134    703
  Planarity :  0.005   0.043    824
  Dihedral  :  4.406  20.985    619
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.46
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.31), residues: 576
  helix: -0.76 (0.24), residues: 391
  sheet:  None (None), residues: 0
  loop : -2.26 (0.38), residues: 185

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 4688)
  covalent geometry    : angle       0.52411 ( 6324)
  SS BOND              : bond        0.00209 (   13)
  SS BOND              : angle       0.98414 (   26)
  hydrogen bonds       : bond        0.03382 (  251)
  hydrogen bonds       : angle       3.94000 (  741)

*********************** 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
  9 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8640 (mmp) cc_final: 0.8421 (mmm)
REVERT: A  123 MET cc_start: 0.8908 (pmm) cc_final: 0.8682 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0417
  time to fit residues: 0.6840
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0770
   overall best weight:    0.5340

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.053228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043324 restraints weight = 35125.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.044555 restraints weight = 18340.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.045471 restraints weight = 12158.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.046049 restraints weight = 9280.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.046240 restraints weight = 7790.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1536

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= 0.085
  Angle     :  0.473   6.377   6350  Z= 0.244
  Chirality :  0.037   0.127    703
  Planarity :  0.003   0.038    824
  Dihedral  :  3.867  17.179    619
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.35), residues: 576
  helix:  0.47 (0.27), residues: 388
  sheet:  None (None), residues: 0
  loop : -1.85 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.009   0.001   TYR A 370 
 PHE   0.023   0.001   PHE A 554 
 TRP   0.003   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00175 ( 4688)
  covalent geometry    : angle       0.47169 ( 6324)
  SS BOND              : bond        0.00195 (   13)
  SS BOND              : angle       0.69353 (   26)
  hydrogen bonds       : bond        0.02715 (  251)
  hydrogen bonds       : angle       3.51054 (  741)

*********************** 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: 0
    poor density    : 9
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8778 (mmp) cc_final: 0.8573 (mmm)
REVERT: A  123 MET cc_start: 0.8872 (pmm) cc_final: 0.8464 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0613
  time to fit residues: 0.9696
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  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   chunk 53 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 26 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0980
   overall best weight:    1.1560

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.052582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.042531 restraints weight = 35294.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.043788 restraints weight = 18502.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.044606 restraints weight = 12354.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.045201 restraints weight = 9569.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.045363 restraints weight = 8045.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    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 = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1788

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= 0.098
  Angle     :  0.485   8.154   6350  Z= 0.249
  Chirality :  0.037   0.127    703
  Planarity :  0.003   0.036    824
  Dihedral  :  3.746  15.914    619
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 11.07 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.37), residues: 576
  helix:  1.05 (0.28), residues: 390
  sheet:  None (None), residues: 0
  loop : -1.51 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  98 
 TYR   0.009   0.001   TYR A 370 
 PHE   0.032   0.001   PHE A 554 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4688)
  covalent geometry    : angle       0.48477 ( 6324)
  SS BOND              : bond        0.00172 (   13)
  SS BOND              : angle       0.63299 (   26)
  hydrogen bonds       : bond        0.02808 (  251)
  hydrogen bonds       : angle       3.37581 (  741)

*********************** 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
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 10
  average time/residue: 0.0576
  time to fit residues: 1.0658
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  : 0.185 
-------------------------------------------------------------------------------
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 14 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.052525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.042432 restraints weight = 35027.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.043678 restraints weight = 18372.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.044484 restraints weight = 12298.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.044916 restraints weight = 9570.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.045310 restraints weight = 8232.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    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 = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2001

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= 0.095
  Angle     :  0.479   6.539   6350  Z= 0.246
  Chirality :  0.038   0.142    703
  Planarity :  0.003   0.034    824
  Dihedral  :  3.654  14.611    619
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.25 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.37), residues: 576
  helix:  1.34 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.40 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  98 
 TYR   0.010   0.001   TYR A 370 
 PHE   0.010   0.001   PHE A 554 
 TRP   0.003   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4688)
  covalent geometry    : angle       0.47832 ( 6324)
  SS BOND              : bond        0.00154 (   13)
  SS BOND              : angle       0.55984 (   26)
  hydrogen bonds       : bond        0.02702 (  251)
  hydrogen bonds       : angle       3.31028 (  741)

*********************** 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: 3
    poor density    : 8
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.9036 (pmm) cc_final: 0.8738 (pmm)
  outliers start: 3
  outliers final: 2
  residues processed: 11
  average time/residue: 0.0490
  time to fit residues: 1.0156
Evaluate side-chains
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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 17 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.5980
   chunk 50 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.052328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.042124 restraints weight = 35680.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.043364 restraints weight = 18738.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.044202 restraints weight = 12552.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.044768 restraints weight = 9704.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.044939 restraints weight = 8222.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    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 = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4701  Z= 0.103
  Angle     :  0.483   6.278   6350  Z= 0.247
  Chirality :  0.038   0.134    703
  Planarity :  0.003   0.034    824
  Dihedral  :  3.647  14.127    619
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.25 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.37), residues: 576
  helix:  1.44 (0.28), residues: 401
  sheet:  None (None), residues: 0
  loop : -1.45 (0.45), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 145 
 TYR   0.011   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 149 
 TRP   0.003   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4688)
  covalent geometry    : angle       0.48217 ( 6324)
  SS BOND              : bond        0.00154 (   13)
  SS BOND              : angle       0.56194 (   26)
  hydrogen bonds       : bond        0.02767 (  251)
  hydrogen bonds       : angle       3.28967 (  741)

*********************** 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
  13 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 8
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8940 (mmp) cc_final: 0.8720 (tpp)
REVERT: A  123 MET cc_start: 0.9062 (pmm) cc_final: 0.8704 (pmm)
  outliers start: 5
  outliers final: 3
  residues processed: 13
  average time/residue: 0.0351
  time to fit residues: 0.8421
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  : 0.162 
-------------------------------------------------------------------------------
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 7 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.052633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.042414 restraints weight = 35483.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.043667 restraints weight = 18645.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.044519 restraints weight = 12514.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.045081 restraints weight = 9676.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.045257 restraints weight = 8204.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    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 = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2255

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= 0.090
  Angle     :  0.477   7.076   6350  Z= 0.242
  Chirality :  0.038   0.138    703
  Planarity :  0.003   0.033    824
  Dihedral  :  3.567  13.181    619
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.24 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.37), residues: 576
  helix:  1.63 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.32 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 145 
 TYR   0.010   0.001   TYR A 370 
 PHE   0.010   0.001   PHE A 149 
 TRP   0.005   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 4688)
  covalent geometry    : angle       0.47712 ( 6324)
  SS BOND              : bond        0.00155 (   13)
  SS BOND              : angle       0.53742 (   26)
  hydrogen bonds       : bond        0.02520 (  251)
  hydrogen bonds       : angle       3.21947 (  741)

*********************** 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: 4
    poor density    : 9
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8964 (mmp) cc_final: 0.8751 (tpp)
REVERT: A  123 MET cc_start: 0.9061 (pmm) cc_final: 0.8666 (pmm)
  outliers start: 4
  outliers final: 3
  residues processed: 13
  average time/residue: 0.0344
  time to fit residues: 0.8252
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  : 0.114 
-------------------------------------------------------------------------------
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 27 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:    0.4980
   chunk 4 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.4986

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.050991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.040562 restraints weight = 34741.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.041733 restraints weight = 18495.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.042551 restraints weight = 12558.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.043054 restraints weight = 9776.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.043468 restraints weight = 8356.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
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:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4701  Z= 0.167
  Angle     :  0.568   6.516   6350  Z= 0.292
  Chirality :  0.041   0.228    703
  Planarity :  0.003   0.033    824
  Dihedral  :  3.803  14.578    619
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.03 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.37), residues: 576
  helix:  1.44 (0.28), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.38 (0.47), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.013   0.001   TYR A 370 
 PHE   0.019   0.001   PHE A 149 
 TRP   0.005   0.002   TRP A 214 
 HIS   0.004   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4688)
  covalent geometry    : angle       0.56740 ( 6324)
  SS BOND              : bond        0.00178 (   13)
  SS BOND              : angle       0.65863 (   26)
  hydrogen bonds       : bond        0.03493 (  251)
  hydrogen bonds       : angle       3.54958 (  741)

*********************** 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
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 7
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9062 (mmp) cc_final: 0.8860 (tpp)
REVERT: A  123 MET cc_start: 0.9082 (pmm) cc_final: 0.8517 (pmm)
  outliers start: 4
  outliers final: 3
  residues processed: 11
  average time/residue: 0.0390
  time to fit residues: 0.7986
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  : 0.133 
-------------------------------------------------------------------------------
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 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    1.1588

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.051956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.041604 restraints weight = 34451.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.042847 restraints weight = 18204.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.043677 restraints weight = 12241.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044101 restraints weight = 9506.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.044579 restraints weight = 8192.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    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 = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      610 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2524

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= 0.099
  Angle     :  0.500   7.278   6350  Z= 0.255
  Chirality :  0.039   0.233    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.725  17.391    619
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 14.43 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.37), residues: 576
  helix:  1.68 (0.28), residues: 399
  sheet:  None (None), residues: 0
  loop : -1.29 (0.45), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 145 
 TYR   0.011   0.001   TYR A 370 
 PHE   0.015   0.001   PHE A 554 
 TRP   0.006   0.001   TRP A 214 
 HIS   0.002   0.000   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 4688)
  covalent geometry    : angle       0.49984 ( 6324)
  SS BOND              : bond        0.00161 (   13)
  SS BOND              : angle       0.58909 (   26)
  hydrogen bonds       : bond        0.02743 (  251)
  hydrogen bonds       : angle       3.33198 (  741)

*********************** 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
  10 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 7
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.9084 (pmm) cc_final: 0.8495 (pmm)
REVERT: A  446 MET cc_start: 0.7496 (mmm) cc_final: 0.7141 (tpp)
  outliers start: 3
  outliers final: 3
  residues processed: 10
  average time/residue: 0.0431
  time to fit residues: 0.8286
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  : 0.117 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.051655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.041202 restraints weight = 34413.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.042434 restraints weight = 18219.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.043248 restraints weight = 12233.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.043822 restraints weight = 9483.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.043986 restraints weight = 8008.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    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 = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4701  Z= 0.116
  Angle     :  0.533   8.768   6350  Z= 0.270
  Chirality :  0.039   0.236    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.698  13.656    619
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.23 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.37), residues: 576
  helix:  1.68 (0.28), residues: 400
  sheet:  None (None), residues: 0
  loop : -1.23 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.012   0.001   TYR A 370 
 PHE   0.015   0.001   PHE A 554 
 TRP   0.004   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4688)
  covalent geometry    : angle       0.53272 ( 6324)
  SS BOND              : bond        0.00167 (   13)
  SS BOND              : angle       0.58356 (   26)
  hydrogen bonds       : bond        0.02954 (  251)
  hydrogen bonds       : angle       3.36074 (  741)

********************** 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
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 7
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.9074 (pmm) cc_final: 0.8660 (pmm)
  outliers start: 4
  outliers final: 4
  residues processed: 11
  average time/residue: 0.0546
  time to fit residues: 1.0857
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  : 0.140 
-------------------------------------------------------------------------------
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 18 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.050102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.039525 restraints weight = 35147.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.040654 restraints weight = 19000.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041406 restraints weight = 12998.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.041928 restraints weight = 10211.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.042080 restraints weight = 8735.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    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 = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4701  Z= 0.248
  Angle     :  0.656   7.056   6350  Z= 0.338
  Chirality :  0.043   0.202    703
  Planarity :  0.004   0.038    824
  Dihedral  :  4.098  16.958    619
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.36), residues: 576
  helix:  1.29 (0.27), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.25 (0.46), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 485 
 TYR   0.015   0.002   TYR A 370 
 PHE   0.023   0.002   PHE A 149 
 TRP   0.007   0.002   TRP A 214 
 HIS   0.006   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 4688)
  covalent geometry    : angle       0.65539 ( 6324)
  SS BOND              : bond        0.00269 (   13)
  SS BOND              : angle       0.81867 (   26)
  hydrogen bonds       : bond        0.04014 (  251)
  hydrogen bonds       : angle       3.90069 (  741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 816.84 seconds
wall clock time: 14 minutes 38.92 seconds (878.92 seconds total)