Starting phenix.real_space_refine
on Thu Jun  5 01:34:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hrn_34979/06_2025/8hrn_34979.cif"
  }
  resolution = 3.9
  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=   0.037 sd=   0.100
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      29      5.16       5
     C    3115      2.51       5
     N     806      2.21       5
     O     920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
  Time building chain proxies: 3.50, per 1000 atoms: 0.72
  Number of scatterers: 4870
  At special positions: 0
  Unit cell: (84.0942, 85.1324, 71.6358, 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      29     16.00
     O     920      8.00
     N     806      7.00
     C    3115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04

  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: 1.26
  Conformation dependent library (CDL) restraints added in 550.2 milliseconds
  

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      65.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 34
    Processing helix  chain 'A' and resid 35 through 53
      removed outlier: 3.588A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.779A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.921A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.569A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.747A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 154
      removed outlier: 3.560A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 172
      removed outlier: 3.964A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.567A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 220 through 249
      removed outlier: 3.887A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.756A  pdb=" N   MET A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 299
      removed outlier: 4.227A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ASP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.954A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.003A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.792A  pdb=" N   ALA A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 3.718A  pdb=" N   VAL A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.648A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.208A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 474 through 482
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.686A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.896A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.611A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.389A  pdb=" N   VAL A 132 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 142 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.452A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.500A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU A 359 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   ASP A 350 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   ARG A 357 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    645 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: 1.38

  Time building geometry restraints manager: 1.50 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: 1575
        1.34 -     1.46: 1252
        1.46 -     1.58: 2129
        1.58 -     1.70: 1
        1.70 -     1.82: 50
  Bond restraints: 5007
  Sorted by residual:
  bond pdb=" CB  PRO A 565 "
       pdb=" CG  PRO A 565 "
    ideal  model  delta    sigma   weight residual
    1.492  1.655 -0.163 5.00e-02 4.00e+02 1.06e+01
  bond pdb=" CG  PRO A 565 "
       pdb=" CD  PRO A 565 "
    ideal  model  delta    sigma   weight residual
    1.503  1.412  0.091 3.40e-02 8.65e+02 7.12e+00
  bond pdb=" N   PRO A 565 "
       pdb=" CD  PRO A 565 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 5.88e+00
  bond pdb=" N   PRO A 565 "
       pdb=" CA  PRO A 565 "
    ideal  model  delta    sigma   weight residual
    1.465  1.442  0.023 1.10e-02 8.26e+03 4.23e+00
  bond pdb=" CG  LEU A 595 "
       pdb=" CD1 LEU A 595 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.59e+00
  ... (remaining 5002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 6728
        3.36 -     6.73: 66
        6.73 -    10.09: 8
       10.09 -    13.46: 0
       13.46 -    16.82: 1
  Bond angle restraints: 6803
  Sorted by residual:
  angle pdb=" CA  PRO A 565 "
        pdb=" N   PRO A 565 "
        pdb=" CD  PRO A 565 "
      ideal   model   delta    sigma   weight residual
     112.00   95.18   16.82 1.40e+00 5.10e-01 1.44e+02
  angle pdb=" N   PRO A 565 "
        pdb=" CD  PRO A 565 "
        pdb=" CG  PRO A 565 "
      ideal   model   delta    sigma   weight residual
     103.20   95.37    7.83 1.50e+00 4.44e-01 2.72e+01
  angle pdb=" C   LEU A 267 "
        pdb=" N   GLY A 268 "
        pdb=" CA  GLY A 268 "
      ideal   model   delta    sigma   weight residual
     123.30  119.20    4.10 1.06e+00 8.90e-01 1.49e+01
  angle pdb=" CB  LYS A 476 "
        pdb=" CG  LYS A 476 "
        pdb=" CD  LYS A 476 "
      ideal   model   delta    sigma   weight residual
     111.30  119.28   -7.98 2.30e+00 1.89e-01 1.20e+01
  angle pdb=" CA  PRO A 565 "
        pdb=" CB  PRO A 565 "
        pdb=" CG  PRO A 565 "
      ideal   model   delta    sigma   weight residual
     104.50   98.19    6.31 1.90e+00 2.77e-01 1.10e+01
  ... (remaining 6798 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 2518
       17.90 -    35.80: 349
       35.80 -    53.70: 70
       53.70 -    71.59: 17
       71.59 -    89.49: 5
  Dihedral angle restraints: 2959
    sinusoidal: 1205
      harmonic: 1754
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.70   43.30     1      1.00e+01 1.00e-02 2.61e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.56  -42.56     1      1.00e+01 1.00e-02 2.53e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   GLN A 531 "
           pdb=" CA  GLN A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.07   19.93     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 2956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 548
       0.056 -    0.112: 145
       0.112 -    0.167: 13
       0.167 -    0.223: 3
       0.223 -    0.279: 1
  Chirality restraints: 710
  Sorted by residual:
  chirality pdb=" CB  VAL A 293 "
            pdb=" CA  VAL A 293 "
            pdb=" CG1 VAL A 293 "
            pdb=" CG2 VAL A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  PRO A 565 "
            pdb=" N   PRO A 565 "
            pdb=" C   PRO A 565 "
            pdb=" CB  PRO A 565 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ASP A 206 "
            pdb=" N   ASP A 206 "
            pdb=" C   ASP A 206 "
            pdb=" CB  ASP A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.75e-01
  ... (remaining 707 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 564 "    0.099 5.00e-02 4.00e+02   1.35e-01 2.93e+01
        pdb=" N   PRO A 565 "   -0.233 5.00e-02 4.00e+02
        pdb=" CA  PRO A 565 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 565 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 137 "   -0.043 5.00e-02 4.00e+02   6.59e-02 6.94e+00
        pdb=" N   PRO A 138 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 138 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 138 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 478 "    0.003 2.00e-02 2.50e+03   1.32e-02 4.35e+00
        pdb=" CG  TRP A 478 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 478 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 478 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 478 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 478 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 478 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 478 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 478 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 478 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 89
        2.64 -     3.21: 4883
        3.21 -     3.77: 8361
        3.77 -     4.34: 11050
        4.34 -     4.90: 17182
  Nonbonded interactions: 41565
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" NE2 GLN A  81 "
            pdb=" OD1 ASN A 103 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   LEU A 333 "
            pdb=" OG1 THR A 362 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.198 3.120
  ... (remaining 41560 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.180
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.230
  Find NCS groups from input model:        0.060
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
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   0.163   5010  Z= 0.227
  Angle     :  0.912  16.822   6809  Z= 0.532
  Chirality :  0.050   0.279    710
  Planarity :  0.007   0.135    881
  Dihedral  : 17.072  89.492   1820
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 24.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 21.44 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.15 (0.35), residues: 595
  helix: -0.62 (0.28), residues: 347
  sheet: -1.41 (1.34), residues: 12
  loop : -0.71 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 478 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.020   0.002   PHE A 452 
 TYR   0.027   0.002   TYR A 385 
 ARG   0.005   0.001   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18856 (  225)
  hydrogen bonds       : angle       6.75314 (  645)
  SS BOND              : bond        0.00523 (    3)
  SS BOND              : angle       1.03335 (    6)
  covalent geometry    : bond        0.00508 ( 5007)
  covalent geometry    : angle       0.91215 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7403 (tmm) cc_final: 0.6907 (tmm)
REVERT: A  391 LEU cc_start: 0.6794 (mt) cc_final: 0.6565 (mp)
REVERT: A  476 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7146 (tppp)
  outliers start: 5
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1803
  time to fit residues: 15.1253
Evaluate side-chains
  61 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  597 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:   30.0000
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0270
   chunk 46 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.3844

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.111778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.096973 restraints weight = 18039.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.099492 restraints weight = 11051.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.101348 restraints weight = 7726.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5010  Z= 0.134
  Angle     :  0.662  10.054   6809  Z= 0.332
  Chirality :  0.043   0.194    710
  Planarity :  0.005   0.061    881
  Dihedral  :  5.190  53.413    649
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.60 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.62 (0.35), residues: 595
  helix: -0.21 (0.28), residues: 348
  sheet: -1.51 (1.33), residues: 12
  loop : -0.43 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 525 
 TYR   0.011   0.001   TYR A 516 
 ARG   0.004   0.001   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  225)
  hydrogen bonds       : angle       4.92526 (  645)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.72956 (    6)
  covalent geometry    : bond        0.00302 ( 5007)
  covalent geometry    : angle       0.66173 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7431 (tmm) cc_final: 0.6808 (tmm)
REVERT: A  169 ARG cc_start: 0.6264 (mtt180) cc_final: 0.6013 (mtt180)
REVERT: A  270 MET cc_start: 0.4445 (tpt) cc_final: 0.4220 (tpt)
REVERT: A  340 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.5911 (pp30)
REVERT: A  476 LYS cc_start: 0.7737 (mmmt) cc_final: 0.6792 (tppt)
  outliers start: 12
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1758
  time to fit residues: 17.6038
Evaluate side-chains
  63 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  340 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:   40.0000
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 58 optimal weight:   30.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 HIS ** 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 = 0.4142 r_free = 0.4142 target = 0.108338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.093071 restraints weight = 18597.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.095543 restraints weight = 11327.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.097033 restraints weight = 7921.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5010  Z= 0.182
  Angle     :  0.677  10.041   6809  Z= 0.341
  Chirality :  0.044   0.137    710
  Planarity :  0.005   0.047    881
  Dihedral  :  4.753  20.403    642
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.92 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.35), residues: 595
  helix: -0.25 (0.28), residues: 352
  sheet: -1.30 (1.31), residues: 12
  loop : -0.40 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 473 
 HIS   0.010   0.002   HIS A 417 
 PHE   0.022   0.002   PHE A 452 
 TYR   0.028   0.003   TYR A 237 
 ARG   0.004   0.001   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  225)
  hydrogen bonds       : angle       4.96388 (  645)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       0.99506 (    6)
  covalent geometry    : bond        0.00405 ( 5007)
  covalent geometry    : angle       0.67674 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7699 (tmm) cc_final: 0.7062 (tmm)
REVERT: A  165 TRP cc_start: 0.3797 (t60) cc_final: 0.3418 (t60)
REVERT: A  171 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7512 (pm20)
REVERT: A  267 LEU cc_start: 0.8001 (mt) cc_final: 0.7546 (mt)
REVERT: A  340 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.5977 (pp30)
REVERT: A  579 MET cc_start: 0.8283 (tmm) cc_final: 0.8018 (ppp)
  outliers start: 19
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1529
  time to fit residues: 16.3680
Evaluate side-chains
  69 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  524 GLN
Chi-restraints excluded: chain A residue  545 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 HIS ** 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 = 0.4099 r_free = 0.4099 target = 0.106063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.089846 restraints weight = 18121.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.092723 restraints weight = 10397.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.094716 restraints weight = 6943.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5010  Z= 0.180
  Angle     :  0.673  10.269   6809  Z= 0.339
  Chirality :  0.044   0.164    710
  Planarity :  0.005   0.047    881
  Dihedral  :  4.840  18.478    642
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.87 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.57 (0.35), residues: 595
  helix: -0.23 (0.28), residues: 347
  sheet: -1.44 (1.32), residues: 12
  loop : -0.30 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 477 
 HIS   0.011   0.001   HIS A 417 
 PHE   0.013   0.001   PHE A 452 
 TYR   0.030   0.002   TYR A 237 
 ARG   0.006   0.001   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  225)
  hydrogen bonds       : angle       4.91722 (  645)
  SS BOND              : bond        0.00335 (    3)
  SS BOND              : angle       0.97513 (    6)
  covalent geometry    : bond        0.00405 ( 5007)
  covalent geometry    : angle       0.67305 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 HIS cc_start: 0.8905 (t-90) cc_final: 0.8578 (t-90)
REVERT: A   82 MET cc_start: 0.7815 (tmm) cc_final: 0.7068 (tmm)
REVERT: A  165 TRP cc_start: 0.3268 (t60) cc_final: 0.2516 (t60)
REVERT: A  171 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7916 (pm20)
REVERT: A  267 LEU cc_start: 0.8032 (mt) cc_final: 0.7549 (mt)
REVERT: A  376 MET cc_start: 0.4743 (tpp) cc_final: 0.4497 (mmm)
REVERT: A  477 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.6214 (t-100)
REVERT: A  579 MET cc_start: 0.8427 (tmm) cc_final: 0.8169 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1589
  time to fit residues: 16.6110
Evaluate side-chains
  73 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  477 TRP
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  524 GLN
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  545 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 12 optimal weight:    0.2980
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 265 HIS
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.110202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.093803 restraints weight = 17711.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.096800 restraints weight = 10092.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.098963 restraints weight = 6714.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5010  Z= 0.116
  Angle     :  0.613  11.520   6809  Z= 0.302
  Chirality :  0.041   0.154    710
  Planarity :  0.004   0.041    881
  Dihedral  :  4.520  18.955    642
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.96 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.42 (0.36), residues: 595
  helix: -0.20 (0.28), residues: 354
  sheet: -1.22 (1.32), residues: 12
  loop : -0.07 (0.46), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 203 
 HIS   0.011   0.001   HIS A 417 
 PHE   0.010   0.001   PHE A 504 
 TYR   0.019   0.002   TYR A 237 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  225)
  hydrogen bonds       : angle       4.69771 (  645)
  SS BOND              : bond        0.00080 (    3)
  SS BOND              : angle       0.78816 (    6)
  covalent geometry    : bond        0.00260 ( 5007)
  covalent geometry    : angle       0.61240 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 HIS cc_start: 0.8849 (t-90) cc_final: 0.8558 (t-90)
REVERT: A   62 MET cc_start: 0.7299 (ttp) cc_final: 0.7022 (mtm)
REVERT: A   82 MET cc_start: 0.7771 (tmm) cc_final: 0.6999 (tmm)
REVERT: A  165 TRP cc_start: 0.3040 (t60) cc_final: 0.2052 (t60)
REVERT: A  171 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7859 (pm20)
REVERT: A  207 TYR cc_start: 0.7263 (m-10) cc_final: 0.7055 (m-10)
REVERT: A  237 TYR cc_start: 0.7440 (t80) cc_final: 0.7159 (t80)
REVERT: A  267 LEU cc_start: 0.7895 (mt) cc_final: 0.7476 (mt)
REVERT: A  579 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8170 (ppp)
  outliers start: 14
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1666
  time to fit residues: 16.5935
Evaluate side-chains
  70 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  524 GLN
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 24 optimal weight:   30.0000
   chunk 50 optimal weight:    0.8980
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.107033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.090780 restraints weight = 17970.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.093567 restraints weight = 10360.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.095475 restraints weight = 6980.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5010  Z= 0.177
  Angle     :  0.676  11.136   6809  Z= 0.340
  Chirality :  0.044   0.190    710
  Planarity :  0.004   0.042    881
  Dihedral  :  4.690  19.092    642
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.34 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.58 (0.35), residues: 595
  helix: -0.30 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.26 (0.44), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 473 
 HIS   0.011   0.001   HIS A 417 
 PHE   0.011   0.002   PHE A 452 
 TYR   0.015   0.002   TYR A 183 
 ARG   0.005   0.001   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  225)
  hydrogen bonds       : angle       4.82983 (  645)
  SS BOND              : bond        0.00248 (    3)
  SS BOND              : angle       0.83695 (    6)
  covalent geometry    : bond        0.00399 ( 5007)
  covalent geometry    : angle       0.67626 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 HIS cc_start: 0.8825 (t-90) cc_final: 0.8580 (t-90)
REVERT: A   82 MET cc_start: 0.7817 (tmm) cc_final: 0.7017 (tmm)
REVERT: A  169 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6315 (mtt180)
REVERT: A  171 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7865 (pm20)
REVERT: A  270 MET cc_start: 0.4785 (tpp) cc_final: 0.4225 (tpp)
REVERT: A  340 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6380 (pp30)
REVERT: A  477 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.6410 (t-100)
REVERT: A  579 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8194 (ppp)
  outliers start: 19
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1567
  time to fit residues: 16.3026
Evaluate side-chains
  69 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  477 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 56 optimal weight:    0.1980
   chunk 53 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.109504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.092947 restraints weight = 17758.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.096020 restraints weight = 10228.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.098093 restraints weight = 6820.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5010  Z= 0.132
  Angle     :  0.651  11.536   6809  Z= 0.324
  Chirality :  0.045   0.338    710
  Planarity :  0.004   0.044    881
  Dihedral  :  4.613  19.191    642
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.24 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.32 (0.36), residues: 595
  helix: -0.10 (0.28), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.14 (0.44), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 203 
 HIS   0.011   0.001   HIS A 417 
 PHE   0.014   0.001   PHE A 523 
 TYR   0.044   0.002   TYR A 237 
 ARG   0.002   0.000   ARG A 518 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  225)
  hydrogen bonds       : angle       4.68361 (  645)
  SS BOND              : bond        0.00125 (    3)
  SS BOND              : angle       0.74325 (    6)
  covalent geometry    : bond        0.00295 ( 5007)
  covalent geometry    : angle       0.65125 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7451 (mtm)
REVERT: A   82 MET cc_start: 0.7805 (tmm) cc_final: 0.7074 (tmm)
REVERT: A  270 MET cc_start: 0.5134 (tpp) cc_final: 0.4866 (mmm)
REVERT: A  340 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6544 (pp30)
REVERT: A  518 ARG cc_start: 0.8498 (ptm-80) cc_final: 0.8287 (ptm-80)
REVERT: A  579 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8160 (ppp)
  outliers start: 18
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1660
  time to fit residues: 15.8373
Evaluate side-chains
  71 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 7 optimal weight:   20.0000
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    4.0788

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.106825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.089945 restraints weight = 17980.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.092887 restraints weight = 10573.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.094971 restraints weight = 7126.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5010  Z= 0.177
  Angle     :  0.714  11.225   6809  Z= 0.352
  Chirality :  0.046   0.287    710
  Planarity :  0.005   0.095    881
  Dihedral  :  4.828  21.356    642
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 25.05 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.39 (0.36), residues: 595
  helix: -0.12 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop : -0.25 (0.43), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 473 
 HIS   0.010   0.001   HIS A 417 
 PHE   0.012   0.002   PHE A 452 
 TYR   0.033   0.002   TYR A 237 
 ARG   0.006   0.001   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  225)
  hydrogen bonds       : angle       4.79919 (  645)
  SS BOND              : bond        0.00274 (    3)
  SS BOND              : angle       0.83295 (    6)
  covalent geometry    : bond        0.00398 ( 5007)
  covalent geometry    : angle       0.71384 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7448 (mtm)
REVERT: A   82 MET cc_start: 0.7876 (tmm) cc_final: 0.7161 (tmm)
REVERT: A  340 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6651 (pp30)
REVERT: A  366 MET cc_start: 0.6697 (mpp) cc_final: 0.6240 (mpp)
REVERT: A  455 MET cc_start: 0.7998 (ttt) cc_final: 0.7786 (ttm)
REVERT: A  477 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.6441 (t-100)
REVERT: A  518 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.7762 (ptm-80)
REVERT: A  579 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8122 (ppp)
  outliers start: 19
  outliers final: 11
  residues processed: 76
  average time/residue: 0.1787
  time to fit residues: 17.8890
Evaluate side-chains
  74 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  477 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 33 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.109264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.093605 restraints weight = 16744.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.096479 restraints weight = 9537.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.098592 restraints weight = 6286.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5010  Z= 0.140
  Angle     :  0.689  11.972   6809  Z= 0.338
  Chirality :  0.044   0.173    710
  Planarity :  0.005   0.069    881
  Dihedral  :  4.729  21.053    642
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.81 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.29 (0.36), residues: 595
  helix: -0.06 (0.28), residues: 350
  sheet:  None (None), residues: 0
  loop : -0.18 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 203 
 HIS   0.008   0.001   HIS A 417 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.029   0.002   TYR A 237 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  225)
  hydrogen bonds       : angle       4.70873 (  645)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       0.77426 (    6)
  covalent geometry    : bond        0.00320 ( 5007)
  covalent geometry    : angle       0.68890 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7435 (mtm)
REVERT: A   82 MET cc_start: 0.7849 (tmm) cc_final: 0.7149 (tmm)
REVERT: A  446 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7630 (mm)
REVERT: A  477 TRP cc_start: 0.7538 (OUTLIER) cc_final: 0.6395 (t-100)
REVERT: A  481 LYS cc_start: 0.7067 (pttm) cc_final: 0.6005 (ttpt)
REVERT: A  518 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.7994 (ptm-80)
REVERT: A  579 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8175 (ppp)
  outliers start: 15
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1781
  time to fit residues: 17.2892
Evaluate side-chains
  75 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  477 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0470
   chunk 35 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0050
   chunk 34 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
A 493 HIS
A 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.112212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.095804 restraints weight = 17795.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.098774 restraints weight = 10419.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.100922 restraints weight = 7043.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5010  Z= 0.124
  Angle     :  0.698  12.709   6809  Z= 0.337
  Chirality :  0.043   0.179    710
  Planarity :  0.004   0.058    881
  Dihedral  :  4.523  22.546    642
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 27.70 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.23 (0.36), residues: 595
  helix: -0.06 (0.28), residues: 345
  sheet:  None (None), residues: 0
  loop : -0.05 (0.44), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 275 
 HIS   0.015   0.001   HIS A 417 
 PHE   0.011   0.001   PHE A 523 
 TYR   0.027   0.002   TYR A 237 
 ARG   0.005   0.001   ARG A 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  225)
  hydrogen bonds       : angle       4.61414 (  645)
  SS BOND              : bond        0.00072 (    3)
  SS BOND              : angle       0.85917 (    6)
  covalent geometry    : bond        0.00271 ( 5007)
  covalent geometry    : angle       0.69777 ( 6803)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7417 (mtm)
REVERT: A   82 MET cc_start: 0.7863 (tmm) cc_final: 0.7387 (tmm)
REVERT: A  169 ARG cc_start: 0.5649 (mtt180) cc_final: 0.4722 (ptt-90)
REVERT: A  446 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7192 (mm)
REVERT: A  556 ASN cc_start: 0.8630 (m-40) cc_final: 0.8380 (m110)
REVERT: A  579 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (ppp)
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1720
  time to fit residues: 16.6913
Evaluate side-chains
  71 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 55 optimal weight:    6.9990
   chunk 14 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.111041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.094296 restraints weight = 18155.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.097352 restraints weight = 10650.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.099486 restraints weight = 7167.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5010  Z= 0.130
  Angle     :  0.702  12.805   6809  Z= 0.340
  Chirality :  0.043   0.169    710
  Planarity :  0.004   0.042    881
  Dihedral  :  4.564  20.937    642
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 28.65 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.18 (0.36), residues: 595
  helix: -0.02 (0.28), residues: 345
  sheet:  None (None), residues: 0
  loop : -0.03 (0.45), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 275 
 HIS   0.015   0.002   HIS A 417 
 PHE   0.017   0.001   PHE A 464 
 TYR   0.026   0.002   TYR A 237 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  225)
  hydrogen bonds       : angle       4.70987 (  645)
  SS BOND              : bond        0.00052 (    3)
  SS BOND              : angle       0.82828 (    6)
  covalent geometry    : bond        0.00293 ( 5007)
  covalent geometry    : angle       0.70147 ( 6803)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1724.18 seconds
wall clock time: 30 minutes 41.03 seconds (1841.03 seconds total)