Starting phenix.real_space_refine
on Thu Mar  6 01:48:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2025/7ryq_24745.cif"
  }
  resolution = 4.6
  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=   0.000 sd=   0.012
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      25      5.16       5
     C    2773      2.51       5
     N     744      2.21       5
     O     790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4332
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 4332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4332
          Classifications: {'peptide': 527}
          Link IDs: {'PTRANS': 15, 'TRANS': 511}
          Chain breaks: 5
  Time building chain proxies: 3.54, per 1000 atoms: 0.82
  Number of scatterers: 4332
  At special positions: 0
  Unit cell: (75.46, 74.48, 142.1, 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      25     16.00
     O     790      8.00
     N     744      7.00
     C    2773      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 480.1 milliseconds
  

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 21
      removed outlier: 3.993A  pdb=" N   ALA B  18 " --> pdb=" O   GLN B  14 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 51
      removed outlier: 3.725A  pdb=" N   LEU B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 95
      removed outlier: 3.730A  pdb=" N   ALA B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 105
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 136 through 152
      removed outlier: 3.599A  pdb=" N   ASN B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ASN B 144 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 148 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP B 149 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU B 151 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
      removed outlier: 3.761A  pdb=" N   ALA B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR B 161 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   MET B 173 " --> pdb=" O   TYR B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 206
    Processing helix  chain 'B' and resid 206 through 219
      removed outlier: 3.856A  pdb=" N   ASN B 210 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 216 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 217 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.507A  pdb=" N   LYS B 236 " --> pdb=" O   HIS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 264
      removed outlier: 4.241A  pdb=" N   ASN B 252 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR B 255 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLN B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   PHE B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TYR B 260 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 280
      removed outlier: 5.374A  pdb=" N   HIS B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   CYS B 272 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASN B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ILE B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   PHE B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing helix  chain 'B' and resid 306 through 325
      removed outlier: 3.670A  pdb=" N   ILE B 310 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TRP B 314 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE B 315 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS B 316 " --> pdb=" O   ARG B 312 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 321 " --> pdb=" O   TYR B 317 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 346 through 364
      removed outlier: 3.568A  pdb=" N   LYS B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLU B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLU B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU B 356 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 359 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLN B 364 " --> pdb=" O   LYS B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 381
    Processing helix  chain 'B' and resid 389 through 410
      removed outlier: 4.989A  pdb=" N   VAL B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 434
      removed outlier: 3.628A  pdb=" N   HIS B 419 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 460
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 464 through 492
    Processing helix  chain 'B' and resid 500 through 525
    Processing helix  chain 'B' and resid 539 through 555
    Processing helix  chain 'B' and resid 560 through 584
      removed outlier: 3.923A  pdb=" N   GLU B 565 " --> pdb=" O   ASP B 561 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 566 " --> pdb=" O   PRO B 562 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 621
      Proline residue:  B 608  - end of helix

    274 hydrogen bonds defined for protein.
    822 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: 1.15

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1400
        1.34 -     1.46: 788
        1.46 -     1.58: 2192
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 4419
  Sorted by residual:
  bond pdb=" CA  ARG B 385 "
       pdb=" CB  ARG B 385 "
    ideal  model  delta    sigma   weight residual
    1.526  1.545 -0.019 9.30e-03 1.16e+04 4.16e+00
  bond pdb=" N   GLU B 109 "
       pdb=" CA  GLU B 109 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.32e-02 5.74e+03 2.75e+00
  bond pdb=" CA  PRO B 527 "
       pdb=" C   PRO B 527 "
    ideal  model  delta    sigma   weight residual
    1.517  1.538 -0.021 1.46e-02 4.69e+03 2.10e+00
  bond pdb=" CA  PHE B 203 "
       pdb=" CB  PHE B 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.550 -0.022 1.56e-02 4.11e+03 1.90e+00
  bond pdb=" CA  LEU B 111 "
       pdb=" C   LEU B 111 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 1.12e-02 7.97e+03 1.88e+00
  ... (remaining 4414 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 5786
        2.87 -     5.74: 148
        5.74 -     8.62: 14
        8.62 -    11.49: 1
       11.49 -    14.36: 2
  Bond angle restraints: 5951
  Sorted by residual:
  angle pdb=" N   ASN B 528 "
        pdb=" CA  ASN B 528 "
        pdb=" C   ASN B 528 "
      ideal   model   delta    sigma   weight residual
     109.41  123.29  -13.88 1.52e+00 4.33e-01 8.34e+01
  angle pdb=" N   LYS B 205 "
        pdb=" CA  LYS B 205 "
        pdb=" C   LYS B 205 "
      ideal   model   delta    sigma   weight residual
     110.80  125.16  -14.36 2.13e+00 2.20e-01 4.55e+01
  angle pdb=" N   VAL B 381 "
        pdb=" CA  VAL B 381 "
        pdb=" C   VAL B 381 "
      ideal   model   delta    sigma   weight residual
     112.98  106.45    6.53 1.25e+00 6.40e-01 2.73e+01
  angle pdb=" N   PRO B 527 "
        pdb=" CA  PRO B 527 "
        pdb=" C   PRO B 527 "
      ideal   model   delta    sigma   weight residual
     113.53  120.63   -7.10 1.39e+00 5.18e-01 2.61e+01
  angle pdb=" N   LYS B 350 "
        pdb=" CA  LYS B 350 "
        pdb=" C   LYS B 350 "
      ideal   model   delta    sigma   weight residual
     111.28  116.24   -4.96 1.09e+00 8.42e-01 2.07e+01
  ... (remaining 5946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2406
       17.34 -    34.69: 216
       34.69 -    52.03: 61
       52.03 -    69.37: 13
       69.37 -    86.71: 6
  Dihedral angle restraints: 2702
    sinusoidal: 1126
      harmonic: 1576
  Sorted by residual:
  dihedral pdb=" CA  LEU B  94 "
           pdb=" C   LEU B  94 "
           pdb=" N   ALA B  95 "
           pdb=" CA  ALA B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.28  -28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  GLU B 437 "
           pdb=" C   GLU B 437 "
           pdb=" N   THR B 438 "
           pdb=" CA  THR B 438 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.71  -25.29     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASP B 388 "
           pdb=" C   ASP B 388 "
           pdb=" N   PHE B 389 "
           pdb=" CA  PHE B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.25  -23.75     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 535
       0.068 -    0.135: 96
       0.135 -    0.202: 14
       0.202 -    0.270: 4
       0.270 -    0.337: 3
  Chirality restraints: 652
  Sorted by residual:
  chirality pdb=" CA  LYS B 205 "
            pdb=" N   LYS B 205 "
            pdb=" C   LYS B 205 "
            pdb=" CB  LYS B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" CA  GLU B 109 "
            pdb=" N   GLU B 109 "
            pdb=" C   GLU B 109 "
            pdb=" CB  GLU B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO B 527 "
            pdb=" N   PRO B 527 "
            pdb=" C   PRO B 527 "
            pdb=" CB  PRO B 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 649 not shown)

  Planarity restraints: 758
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  51 "   -0.052 5.00e-02 4.00e+02   7.87e-02 9.92e+00
        pdb=" N   PRO B  52 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO B  52 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B  52 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 578 "    0.026 2.00e-02 2.50e+03   2.18e-02 8.28e+00
        pdb=" CG  PHE B 578 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 578 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 578 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 578 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 578 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 578 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 526 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO B 527 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 527 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 527 "    0.036 5.00e-02 4.00e+02
  ... (remaining 755 not shown)

  Histogram of nonbonded interaction distances:
        1.25 -     1.98: 7
        1.98 -     2.71: 275
        2.71 -     3.44: 7338
        3.44 -     4.17: 10282
        4.17 -     4.90: 17111
  Nonbonded interactions: 35013
  Sorted by model distance:
  nonbonded pdb=" CA  SER B 523 "
            pdb=" CG  PRO B 527 "
     model   vdw
     1.251 3.870
  nonbonded pdb=" N   SER B 523 "
            pdb=" CG  PRO B 527 "
     model   vdw
     1.404 3.520
  nonbonded pdb=" O   ASP B 522 "
            pdb=" CD  PRO B 527 "
     model   vdw
     1.613 3.440
  nonbonded pdb=" NE  ARG B 525 "
            pdb=" OE1 GLU B 533 "
     model   vdw
     1.718 3.120
  nonbonded pdb=" CD  ARG B 525 "
            pdb=" OE1 GLU B 533 "
     model   vdw
     1.721 3.440
  ... (remaining 35008 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.600
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
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   0.048   4419  Z= 0.327
  Angle     :  1.083  14.362   5951  Z= 0.668
  Chirality :  0.058   0.337    652
  Planarity :  0.007   0.079    758
  Dihedral  : 15.485  86.712   1674
  Min Nonbonded Distance : 1.251

Molprobity Statistics.
  All-atom Clashscore : 39.25
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.68 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  :  3.23 %
    Favored  : 90.52 %
  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: -1.51 (0.36), residues: 515
  helix: -0.47 (0.25), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.28 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 314 
 HIS   0.008   0.002   HIS B 447 
 PHE   0.050   0.004   PHE B 578 
 TYR   0.026   0.003   TYR B 516 
 ARG   0.009   0.001   ARG B 270 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  330 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8296 (mm-40)
REVERT: B  335 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9039 (mm-30)
REVERT: B  397 LEU cc_start: 0.9336 (tt) cc_final: 0.9102 (mt)
REVERT: B  486 ASP cc_start: 0.8766 (m-30) cc_final: 0.8514 (m-30)
  outliers start: 29
  outliers final: 12
  residues processed: 82
  average time/residue: 0.2316
  time to fit residues: 22.5285
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.067456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.057841 restraints weight = 45614.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.058857 restraints weight = 29287.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.059637 restraints weight = 21153.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4419  Z= 0.234
  Angle     :  0.816  13.926   5951  Z= 0.428
  Chirality :  0.048   0.373    652
  Planarity :  0.006   0.063    758
  Dihedral  :  6.484  28.111    579
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.96 %
    Favored  : 94.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.36), residues: 515
  helix: -0.08 (0.25), residues: 385
  sheet:  None (None), residues: 0
  loop : -2.52 (0.53), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 314 
 HIS   0.004   0.001   HIS B 447 
 PHE   0.027   0.003   PHE B 578 
 TYR   0.024   0.002   TYR B 317 
 ARG   0.010   0.001   ARG B 525 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9368 (mm) cc_final: 0.9098 (mm)
REVERT: B  210 ASN cc_start: 0.9257 (m110) cc_final: 0.8931 (t0)
REVERT: B  329 MET cc_start: 0.9050 (pmm) cc_final: 0.8668 (pmm)
REVERT: B  486 ASP cc_start: 0.8852 (m-30) cc_final: 0.8580 (m-30)
REVERT: B  548 PHE cc_start: 0.8761 (m-80) cc_final: 0.8456 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2210
  time to fit residues: 15.1709
Evaluate side-chains
  41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.057234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.046464 restraints weight = 49155.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.047473 restraints weight = 35915.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.048225 restraints weight = 28358.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4419  Z= 0.296
  Angle     :  0.835  13.006   5951  Z= 0.449
  Chirality :  0.048   0.337    652
  Planarity :  0.006   0.071    758
  Dihedral  :  6.549  28.220    579
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 25.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.09 %
    Favored  : 95.69 %
  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: -0.93 (0.36), residues: 515
  helix:  0.09 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -2.53 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 314 
 HIS   0.013   0.002   HIS B 447 
 PHE   0.021   0.003   PHE B 430 
 TYR   0.020   0.002   TYR B  33 
 ARG   0.007   0.001   ARG B 443 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9473 (mm) cc_final: 0.9202 (mm)
REVERT: B  210 ASN cc_start: 0.9294 (m110) cc_final: 0.8943 (t0)
REVERT: B  329 MET cc_start: 0.9212 (pmm) cc_final: 0.8792 (pmm)
REVERT: B  393 ARG cc_start: 0.9159 (mpt-90) cc_final: 0.8564 (mmm160)
REVERT: B  419 HIS cc_start: 0.8872 (m-70) cc_final: 0.8389 (m90)
REVERT: B  548 PHE cc_start: 0.8816 (m-10) cc_final: 0.8544 (m-80)
REVERT: B  549 ARG cc_start: 0.9036 (ptm-80) cc_final: 0.8726 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2136
  time to fit residues: 13.2044
Evaluate side-chains
  38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 23 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.067360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.057904 restraints weight = 46092.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.059001 restraints weight = 28675.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.059783 restraints weight = 20336.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4419  Z= 0.199
  Angle     :  0.729  10.790   5951  Z= 0.382
  Chirality :  0.045   0.304    652
  Planarity :  0.005   0.054    758
  Dihedral  :  6.255  28.234    579
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.66 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.37), residues: 515
  helix:  0.23 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop : -2.82 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 314 
 HIS   0.006   0.001   HIS B 271 
 PHE   0.042   0.002   PHE B  13 
 TYR   0.017   0.002   TYR B 317 
 ARG   0.008   0.001   ARG B 393 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9388 (mm) cc_final: 0.9068 (mm)
REVERT: B  210 ASN cc_start: 0.9209 (m110) cc_final: 0.8922 (t0)
REVERT: B  329 MET cc_start: 0.9178 (pmm) cc_final: 0.8713 (pmm)
REVERT: B  398 LEU cc_start: 0.9181 (mt) cc_final: 0.8945 (pp)
REVERT: B  419 HIS cc_start: 0.8746 (m-70) cc_final: 0.8261 (m90)
REVERT: B  486 ASP cc_start: 0.8803 (m-30) cc_final: 0.8577 (m-30)
REVERT: B  548 PHE cc_start: 0.8748 (m-10) cc_final: 0.8456 (m-80)
REVERT: B  549 ARG cc_start: 0.8971 (ptm-80) cc_final: 0.8703 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1992
  time to fit residues: 13.1123
Evaluate side-chains
  39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 28 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0770
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 209 HIS
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.068589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.058981 restraints weight = 46717.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.060067 restraints weight = 29313.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.060849 restraints weight = 20834.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4419  Z= 0.185
  Angle     :  0.708  12.328   5951  Z= 0.370
  Chirality :  0.045   0.371    652
  Planarity :  0.005   0.053    758
  Dihedral  :  5.962  28.069    579
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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: -0.53 (0.37), residues: 515
  helix:  0.47 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop : -2.86 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 314 
 HIS   0.003   0.001   HIS B 447 
 PHE   0.026   0.002   PHE B 409 
 TYR   0.018   0.001   TYR B 482 
 ARG   0.005   0.001   ARG B 270 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9340 (mm) cc_final: 0.8984 (mm)
REVERT: B  210 ASN cc_start: 0.9157 (m110) cc_final: 0.8809 (t0)
REVERT: B  329 MET cc_start: 0.9159 (pmm) cc_final: 0.8703 (pmm)
REVERT: B  419 HIS cc_start: 0.8686 (m-70) cc_final: 0.8203 (m90)
REVERT: B  441 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8789 (mp0)
REVERT: B  484 MET cc_start: 0.9522 (mmp) cc_final: 0.9306 (ptt)
REVERT: B  486 ASP cc_start: 0.8834 (m-30) cc_final: 0.8586 (m-30)
REVERT: B  548 PHE cc_start: 0.8742 (m-10) cc_final: 0.8423 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2052
  time to fit residues: 14.3007
Evaluate side-chains
  42 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.061059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.049918 restraints weight = 44978.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.051118 restraints weight = 30208.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.052039 restraints weight = 22790.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4419  Z= 0.193
  Angle     :  0.694  11.087   5951  Z= 0.367
  Chirality :  0.044   0.291    652
  Planarity :  0.005   0.067    758
  Dihedral  :  5.864  29.194    579
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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: -0.55 (0.36), residues: 515
  helix:  0.45 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -2.76 (0.50), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 314 
 HIS   0.008   0.001   HIS B 479 
 PHE   0.016   0.002   PHE B 203 
 TYR   0.016   0.002   TYR B 482 
 ARG   0.004   0.001   ARG B 270 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9415 (mm) cc_final: 0.9155 (mm)
REVERT: B  210 ASN cc_start: 0.9245 (m110) cc_final: 0.8851 (t0)
REVERT: B  419 HIS cc_start: 0.8845 (m-70) cc_final: 0.8372 (m90)
REVERT: B  441 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8946 (mp0)
REVERT: B  453 MET cc_start: 0.8417 (ppp) cc_final: 0.7950 (ppp)
REVERT: B  484 MET cc_start: 0.9555 (mmp) cc_final: 0.9343 (ptt)
REVERT: B  486 ASP cc_start: 0.8905 (m-30) cc_final: 0.8661 (m-30)
REVERT: B  548 PHE cc_start: 0.8770 (m-10) cc_final: 0.8493 (m-80)
REVERT: B  549 ARG cc_start: 0.9023 (ptm-80) cc_final: 0.8756 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.2056
  time to fit residues: 12.8226
Evaluate side-chains
  37 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0030
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.068845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.059055 restraints weight = 46204.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.060188 restraints weight = 28858.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.060968 restraints weight = 20495.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4419  Z= 0.175
  Angle     :  0.702  12.664   5951  Z= 0.365
  Chirality :  0.045   0.414    652
  Planarity :  0.005   0.059    758
  Dihedral  :  5.742  30.756    579
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    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: -0.31 (0.37), residues: 515
  helix:  0.66 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.77 (0.51), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 314 
 HIS   0.007   0.001   HIS B 479 
 PHE   0.023   0.002   PHE B 409 
 TYR   0.018   0.001   TYR B 482 
 ARG   0.004   0.001   ARG B 443 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 ASN cc_start: 0.9125 (m110) cc_final: 0.8851 (t0)
REVERT: B  419 HIS cc_start: 0.8860 (m-70) cc_final: 0.8376 (m90)
REVERT: B  450 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7825 (mtp180)
REVERT: B  453 MET cc_start: 0.8281 (ppp) cc_final: 0.7836 (ppp)
REVERT: B  484 MET cc_start: 0.9509 (mmp) cc_final: 0.9300 (ptt)
REVERT: B  486 ASP cc_start: 0.8838 (m-30) cc_final: 0.8590 (m-30)
REVERT: B  548 PHE cc_start: 0.8753 (m-10) cc_final: 0.8506 (m-80)
REVERT: B  549 ARG cc_start: 0.8990 (ptm-80) cc_final: 0.8646 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1919
  time to fit residues: 12.0583
Evaluate side-chains
  37 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.2980
   chunk 20 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.068313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.058563 restraints weight = 45540.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.059603 restraints weight = 28495.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.060375 restraints weight = 20404.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4419  Z= 0.177
  Angle     :  0.706  11.663   5951  Z= 0.369
  Chirality :  0.044   0.345    652
  Planarity :  0.005   0.056    758
  Dihedral  :  5.632  30.810    579
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    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: -0.27 (0.37), residues: 515
  helix:  0.70 (0.26), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.78 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 314 
 HIS   0.005   0.001   HIS B 479 
 PHE   0.035   0.002   PHE B 396 
 TYR   0.034   0.002   TYR B 402 
 ARG   0.011   0.001   ARG B 443 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 ASN cc_start: 0.9138 (m110) cc_final: 0.8873 (t0)
REVERT: B  419 HIS cc_start: 0.8871 (m-70) cc_final: 0.8393 (m90)
REVERT: B  453 MET cc_start: 0.8443 (ppp) cc_final: 0.8025 (ppp)
REVERT: B  484 MET cc_start: 0.9513 (mmp) cc_final: 0.9302 (ptt)
REVERT: B  486 ASP cc_start: 0.8848 (m-30) cc_final: 0.8610 (m-30)
REVERT: B  548 PHE cc_start: 0.8764 (m-10) cc_final: 0.8508 (m-80)
REVERT: B  549 ARG cc_start: 0.8956 (ptm-80) cc_final: 0.8621 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1943
  time to fit residues: 11.7498
Evaluate side-chains
  38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.069165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.059187 restraints weight = 45969.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.060350 restraints weight = 29062.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.061162 restraints weight = 20524.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4419  Z= 0.172
  Angle     :  0.686  11.137   5951  Z= 0.355
  Chirality :  0.044   0.327    652
  Planarity :  0.005   0.069    758
  Dihedral  :  5.503  30.289    579
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    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: -0.27 (0.37), residues: 515
  helix:  0.67 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -2.87 (0.51), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 314 
 HIS   0.004   0.001   HIS B 479 
 PHE   0.019   0.002   PHE B 409 
 TYR   0.026   0.001   TYR B 402 
 ARG   0.005   0.001   ARG B 393 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 ASN cc_start: 0.9101 (m110) cc_final: 0.8870 (t0)
REVERT: B  419 HIS cc_start: 0.8831 (m-70) cc_final: 0.8360 (m90)
REVERT: B  453 MET cc_start: 0.8445 (ppp) cc_final: 0.8060 (ppp)
REVERT: B  484 MET cc_start: 0.9509 (mmp) cc_final: 0.9257 (ptt)
REVERT: B  548 PHE cc_start: 0.8791 (m-10) cc_final: 0.8514 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2326
  time to fit residues: 14.2520
Evaluate side-chains
  39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 271 HIS
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.069123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.059289 restraints weight = 44782.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.060406 restraints weight = 28527.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.061155 restraints weight = 20261.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4419  Z= 0.172
  Angle     :  0.689  10.984   5951  Z= 0.357
  Chirality :  0.044   0.316    652
  Planarity :  0.005   0.071    758
  Dihedral  :  5.493  30.132    579
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    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: -0.17 (0.37), residues: 515
  helix:  0.75 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -2.70 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 314 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.010   0.001   PHE B 430 
 TYR   0.024   0.001   TYR B 402 
 ARG   0.009   0.001   ARG B 443 

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

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

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 ASN cc_start: 0.9088 (m110) cc_final: 0.8883 (t0)
REVERT: B  419 HIS cc_start: 0.8788 (m-70) cc_final: 0.8323 (m90)
REVERT: B  453 MET cc_start: 0.8461 (ppp) cc_final: 0.8093 (ppp)
REVERT: B  484 MET cc_start: 0.9496 (mmp) cc_final: 0.9252 (ptt)
REVERT: B  548 PHE cc_start: 0.8806 (m-10) cc_final: 0.8540 (m-80)
REVERT: B  549 ARG cc_start: 0.8956 (ptm-80) cc_final: 0.8607 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2833
  time to fit residues: 17.3941
Evaluate side-chains
  42 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 2.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 330 GLN
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.069005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.059098 restraints weight = 45366.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.060247 restraints weight = 28827.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.061036 restraints weight = 20443.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4419  Z= 0.179
  Angle     :  0.712  10.788   5951  Z= 0.374
  Chirality :  0.044   0.307    652
  Planarity :  0.006   0.112    758
  Dihedral  :  5.475  30.114    579
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    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: -0.15 (0.37), residues: 515
  helix:  0.75 (0.26), residues: 385
  sheet:  None (None), residues: 0
  loop : -2.66 (0.52), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 314 
 HIS   0.009   0.001   HIS B 447 
 PHE   0.020   0.002   PHE B 409 
 TYR   0.024   0.001   TYR B 402 
 ARG   0.010   0.001   ARG B 443 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.91 seconds
wall clock time: 28 minutes 51.20 seconds (1731.20 seconds total)