Starting phenix.real_space_refine
on Sat May 10 02:02:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q3f_18126/05_2025/8q3f_18126.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q3f_18126/05_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_18126/05_2025/8q3f_18126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q3f_18126/05_2025/8q3f_18126.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q3f_18126/05_2025/8q3f_18126.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q3f_18126/05_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-5687/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: 3.07, per 1000 atoms: 0.67
  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: 0.98
  Conformation dependent library (CDL) restraints added in 525.8 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: 0.42
  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: 1.01

  Time building geometry restraints manager: 1.18 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:             0.820
  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:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.060
  Process input model:                     13.780
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.530
-------------------------------------------------------------------------------
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  : 0.582 
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: 0.1396
  time to fit residues: 2.2459
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  : 0.535 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.042863 restraints weight = 34063.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044142 restraints weight = 17886.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.044995 restraints weight = 11835.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
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 = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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  : 0.576 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8684 (mmp) cc_final: 0.8470 (mmm)
REVERT: A  123 MET cc_start: 0.8890 (pmm) cc_final: 0.8658 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1493
  time to fit residues: 2.7979
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  : 0.562 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 37 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.4984

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.053305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.043355 restraints weight = 34265.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.044638 restraints weight = 17858.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.045521 restraints weight = 11823.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1513

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= 0.084
  Angle     :  0.484   7.652   6350  Z= 0.246
  Chirality :  0.037   0.128    703
  Planarity :  0.003   0.038    824
  Dihedral  :  3.874  17.149    619
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  9.88 %
    Favored  : 89.92 %
  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: -0.48 (0.35), residues: 576
  helix:  0.45 (0.27), residues: 388
  sheet:  None (None), residues: 0
  loop : -1.87 (0.41), residues: 188

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   0.023   0.001   PHE A 554 
 TYR   0.009   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02661 (  251)
  hydrogen bonds       : angle       3.52158 (  741)
  SS BOND              : bond        0.00205 (   13)
  SS BOND              : angle       0.68648 (   26)
  covalent geometry    : bond        0.00170 ( 4688)
  covalent geometry    : angle       0.48263 ( 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  : 0.553 
Fit side-chains
REVERT: A   87 MET cc_start: 0.8802 (mmp) cc_final: 0.8601 (mmm)
REVERT: A  123 MET cc_start: 0.8830 (pmm) cc_final: 0.8423 (pmm)
REVERT: A  446 MET cc_start: 0.7185 (mmm) cc_final: 0.6902 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1367
  time to fit residues: 2.2539
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  : 0.684 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0370
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.1862

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.052365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.042318 restraints weight = 34715.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.043569 restraints weight = 18143.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044403 restraints weight = 12065.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    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 = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1779

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     :  0.476   6.370   6350  Z= 0.244
  Chirality :  0.037   0.127    703
  Planarity :  0.003   0.035    824
  Dihedral  :  3.725  15.849    619
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 10.67 %
    Favored  : 89.13 %
  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:  0.34 (0.37), residues: 576
  helix:  1.05 (0.28), residues: 390
  sheet:  None (None), residues: 0
  loop : -1.52 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 
 PHE   0.037   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02836 (  251)
  hydrogen bonds       : angle       3.37905 (  741)
  SS BOND              : bond        0.00172 (   13)
  SS BOND              : angle       0.62881 (   26)
  covalent geometry    : bond        0.00212 ( 4688)
  covalent geometry    : angle       0.47531 ( 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
  9 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 8
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 9
  average time/residue: 0.1474
  time to fit residues: 2.5615
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  : 0.583 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.052459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.042313 restraints weight = 34878.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.043591 restraints weight = 18128.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.044455 restraints weight = 12048.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    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 = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1968

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     :  0.470   6.294   6350  Z= 0.243
  Chirality :  0.037   0.126    703
  Planarity :  0.003   0.034    824
  Dihedral  :  3.631  14.650    619
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.66 %
    Favored  : 87.55 %
  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:  0.70 (0.37), residues: 576
  helix:  1.30 (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   0.003   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 
 PHE   0.038   0.001   PHE A 554 
 TYR   0.010   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02717 (  251)
  hydrogen bonds       : angle       3.30202 (  741)
  SS BOND              : bond        0.00162 (   13)
  SS BOND              : angle       0.57676 (   26)
  covalent geometry    : bond        0.00205 ( 4688)
  covalent geometry    : angle       0.46914 ( 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
  12 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 8
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8993 (pmm) cc_final: 0.8697 (pmm)
  outliers start: 4
  outliers final: 2
  residues processed: 12
  average time/residue: 0.1443
  time to fit residues: 3.1038
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  : 0.526 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 48 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.5782

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.051651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041632 restraints weight = 34092.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.042802 restraints weight = 18233.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.043585 restraints weight = 12312.567|
|-----------------------------------------------------------------------------|
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:      611 |
|-----------------------------------------------------------------------------|
|-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: 0.8094
moved from start:          0.2132

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= 0.114
  Angle     :  0.497   7.504   6350  Z= 0.255
  Chirality :  0.038   0.134    703
  Planarity :  0.003   0.034    824
  Dihedral  :  3.664  14.262    619
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.65 %
    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 (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:  0.86 (0.37), residues: 576
  helix:  1.39 (0.28), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.43 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 464 
 PHE   0.013   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        0.02924 (  251)
  hydrogen bonds       : angle       3.29148 (  741)
  SS BOND              : bond        0.00156 (   13)
  SS BOND              : angle       0.56084 (   26)
  covalent geometry    : bond        0.00253 ( 4688)
  covalent geometry    : angle       0.49717 ( 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: 3
    poor density    : 9
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.8994 (mmp) cc_final: 0.8766 (tpp)
REVERT: A  123 MET cc_start: 0.9058 (pmm) cc_final: 0.8710 (pmm)
  outliers start: 3
  outliers final: 3
  residues processed: 12
  average time/residue: 0.1287
  time to fit residues: 2.8553
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  : 0.534 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 49 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.052562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.042378 restraints weight = 35234.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.043647 restraints weight = 18524.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.044458 restraints weight = 12403.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    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 = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2253

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     :  0.475   7.175   6350  Z= 0.241
  Chirality :  0.038   0.129    703
  Planarity :  0.003   0.033    824
  Dihedral  :  3.592  13.208    619
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.85 %
    Favored  : 86.17 %
  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:  1.14 (0.37), residues: 576
  helix:  1.65 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.27 (0.46), 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   0.032   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        0.02552 (  251)
  hydrogen bonds       : angle       3.21623 (  741)
  SS BOND              : bond        0.00153 (   13)
  SS BOND              : angle       0.54608 (   26)
  covalent geometry    : bond        0.00194 ( 4688)
  covalent geometry    : angle       0.47507 ( 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  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9016 (mmp) cc_final: 0.8791 (tpp)
REVERT: A  123 MET cc_start: 0.9040 (pmm) cc_final: 0.8647 (pmm)
  outliers start: 5
  outliers final: 3
  residues processed: 13
  average time/residue: 0.1290
  time to fit residues: 2.9665
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  : 0.525 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.052242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.042006 restraints weight = 34555.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043256 restraints weight = 18247.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.044078 restraints weight = 12248.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    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 = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2356

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= 0.099
  Angle     :  0.490   7.814   6350  Z= 0.248
  Chirality :  0.038   0.138    703
  Planarity :  0.003   0.032    824
  Dihedral  :  3.574  13.082    619
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.44 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.37), residues: 576
  helix:  1.59 (0.28), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.35 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 464 
 PHE   0.012   0.001   PHE A 149 
 TYR   0.011   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02666 (  251)
  hydrogen bonds       : angle       3.21803 (  741)
  SS BOND              : bond        0.00150 (   13)
  SS BOND              : angle       0.53544 (   26)
  covalent geometry    : bond        0.00216 ( 4688)
  covalent geometry    : angle       0.48940 ( 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
  12 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 8
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9090 (mmp) cc_final: 0.8864 (mmm)
REVERT: A  123 MET cc_start: 0.9070 (pmm) cc_final: 0.8474 (pmm)
  outliers start: 4
  outliers final: 3
  residues processed: 12
  average time/residue: 0.1256
  time to fit residues: 2.9618
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  : 0.559 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   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 = 0.052564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.042333 restraints weight = 35365.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.043591 restraints weight = 18672.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044416 restraints weight = 12524.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    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 = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2400

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= 0.089
  Angle     :  0.492   8.611   6350  Z= 0.248
  Chirality :  0.039   0.235    703
  Planarity :  0.003   0.032    824
  Dihedral  :  3.562  12.719    619
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.83 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.29 (0.37), residues: 576
  helix:  1.76 (0.28), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.21 (0.46), 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   0.016   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        0.02512 (  251)
  hydrogen bonds       : angle       3.22632 (  741)
  SS BOND              : bond        0.00165 (   13)
  SS BOND              : angle       0.53553 (   26)
  covalent geometry    : bond        0.00193 ( 4688)
  covalent geometry    : angle       0.49184 ( 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
  9 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9139 (mmp) cc_final: 0.8934 (tpp)
REVERT: A  123 MET cc_start: 0.9063 (pmm) cc_final: 0.8453 (pmm)
  outliers start: 2
  outliers final: 2
  residues processed: 9
  average time/residue: 0.1508
  time to fit residues: 2.6230
Evaluate side-chains
  9 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 7
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0030
   chunk 53 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.052585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.042538 restraints weight = 33747.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.043781 restraints weight = 17661.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.044649 restraints weight = 11719.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2473

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= 0.085
  Angle     :  0.475   6.605   6350  Z= 0.240
  Chirality :  0.038   0.224    703
  Planarity :  0.003   0.032    824
  Dihedral  :  3.444  12.246    619
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.83 %
    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:  1.48 (0.37), residues: 576
  helix:  1.99 (0.28), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.16 (0.45), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 214 
 HIS   0.001   0.000   HIS A 535 
 PHE   0.014   0.001   PHE A 554 
 TYR   0.009   0.001   TYR A 370 
 ARG   0.001   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02358 (  251)
  hydrogen bonds       : angle       3.14271 (  741)
  SS BOND              : bond        0.00167 (   13)
  SS BOND              : angle       0.51976 (   26)
  covalent geometry    : bond        0.00180 ( 4688)
  covalent geometry    : angle       0.47447 ( 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
  11 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 7
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.9083 (mmp) cc_final: 0.8853 (mmm)
REVERT: A  123 MET cc_start: 0.9051 (pmm) cc_final: 0.8421 (pmm)
  outliers start: 4
  outliers final: 4
  residues processed: 11
  average time/residue: 0.1351
  time to fit residues: 2.8573
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  : 0.596 
-------------------------------------------------------------------------------
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 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0030
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7394

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.052581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.042451 restraints weight = 33844.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.043687 restraints weight = 17820.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.044530 restraints weight = 11869.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
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:      611 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2532

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= 0.086
  Angle     :  0.476   6.879   6350  Z= 0.241
  Chirality :  0.038   0.217    703
  Planarity :  0.003   0.032    824
  Dihedral  :  3.416  12.221    619
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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:  1.53 (0.37), residues: 576
  helix:  2.02 (0.28), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.13 (0.44), residues: 191

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   0.015   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        0.02391 (  251)
  hydrogen bonds       : angle       3.10311 (  741)
  SS BOND              : bond        0.00164 (   13)
  SS BOND              : angle       0.52370 (   26)
  covalent geometry    : bond        0.00184 ( 4688)
  covalent geometry    : angle       0.47555 ( 6324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1655.62 seconds
wall clock time: 29 minutes 42.78 seconds (1782.78 seconds total)