Starting phenix.real_space_refine
on Mon Sep 23 21:59:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/09_2024/7yqm_34029.cif"
  }
  resolution = 2.89
  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=   0.001 sd=   0.036
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    3543      2.51       5
     N    1015      2.21       5
     O    1069      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 5656
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 723, 5656
          Classifications: {'peptide': 723}
          Link IDs: {'PTRANS': 31, 'TRANS': 691}
  Time building chain proxies: 4.18, per 1000 atoms: 0.74
  Number of scatterers: 5656
  At special positions: 0
  Unit cell: (76.446, 81.378, 93.708, 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    1069      8.00
     N    1015      7.00
     C    3543      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: 1.16
  Conformation dependent library (CDL) restraints added in 888.9 milliseconds
  

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      53.0% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 24
    Processing helix  chain 'A' and resid 31 through 71
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 106 through 111
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 159 through 178
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 279 through 296
    Processing helix  chain 'A' and resid 359 through 378
      removed outlier: 4.224A  pdb=" N   TYR A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP A 374 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 414
      removed outlier: 4.033A  pdb=" N   GLU A 398 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 434 through 440
    Processing helix  chain 'A' and resid 453 through 464
    Processing helix  chain 'A' and resid 465 through 468
      removed outlier: 3.573A  pdb=" N   GLY A 468 " --> pdb=" O   MET A 465 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 465 through 468'
    Processing helix  chain 'A' and resid 472 through 478
      removed outlier: 3.812A  pdb=" N   LYS A 477 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 496
      removed outlier: 3.604A  pdb=" N   LYS A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 522
    Processing helix  chain 'A' and resid 523 through 528
    Processing helix  chain 'A' and resid 537 through 551
      removed outlier: 4.384A  pdb=" N   LEU A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   HIS A 547 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR A 548 " --> pdb=" O   HIS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 563 through 567
      removed outlier: 5.878A  pdb=" N   ASN A 566 " --> pdb=" O   THR A 563 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 567 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 563 through 567'
    Processing helix  chain 'A' and resid 568 through 577
    Processing helix  chain 'A' and resid 588 through 613
      removed outlier: 4.039A  pdb=" N   ARG A 609 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 648
    Processing helix  chain 'A' and resid 652 through 671
    Processing helix  chain 'A' and resid 683 through 686
    Processing helix  chain 'A' and resid 687 through 699
    Processing helix  chain 'A' and resid 700 through 707
      Proline residue:  A 704  - end of helix
    Processing helix  chain 'A' and resid 708 through 723
      removed outlier: 3.540A  pdb=" N   HIS A 723 " --> pdb=" O   GLU A 719 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
      removed outlier: 8.214A  pdb=" N   VAL A 348 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ILE A 349 " --> pdb=" O   ILE A 357 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 505
      removed outlier: 6.809A  pdb=" N   ALA A 447 " --> pdb=" O   GLN A 503 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   GLY A 505 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE A 449 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ALA A 447 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   MET A 422 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A 449 " --> pdb=" O   MET A 422 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE A 424 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR A 451 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   ASP A 426 " --> pdb=" O   THR A 451 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL A 386 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   GLY A 423 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE A 388 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   MET A 425 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   LYS A 390 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU A 335 " --> pdb=" O   TYR A 387 " (cutoff:3.500A)
      removed outlier: 8.441A  pdb=" N   VAL A 389 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE A 337 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   THR A 267 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ARG A 338 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A 269 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   GLN A 116 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 137
      removed outlier: 3.540A  pdb=" N   ASP A 258 " --> pdb=" O   GLN A 241 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   HIS A 237 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   THR A 227 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   CYS A 228 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LYS A 232 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   PHE A 216 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   GLY A 221 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 11.966A  pdb=" N   HIS A 318 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 194
      removed outlier: 6.648A  pdb=" N   GLN A 201 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   PHE A 191 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ARG A 199 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   VAL A 193 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   GLN A 197 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA6, first strand: chain 'A' and resid 620 through 621

    289 hydrogen bonds defined for protein.
    834 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: 2.13

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 983
        1.30 -     1.42: 1403
        1.42 -     1.55: 3289
        1.55 -     1.68: 37
        1.68 -     1.81: 52
  Bond restraints: 5764
  Sorted by residual:
  bond pdb=" C   SER A 437 "
       pdb=" O   SER A 437 "
    ideal  model  delta    sigma   weight residual
    1.237  1.169  0.067 1.17e-02 7.31e+03 3.32e+01
  bond pdb=" C   GLU A  49 "
       pdb=" O   GLU A  49 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.29e-02 6.01e+03 1.80e+01
  bond pdb=" CA  ILE A 642 "
       pdb=" CB  ILE A 642 "
    ideal  model  delta    sigma   weight residual
    1.540  1.589 -0.050 1.29e-02 6.01e+03 1.49e+01
  bond pdb=" CA  THR A 209 "
       pdb=" CB  THR A 209 "
    ideal  model  delta    sigma   weight residual
    1.532  1.587 -0.056 1.45e-02 4.76e+03 1.47e+01
  bond pdb=" C   ILE A 642 "
       pdb=" O   ILE A 642 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.039 1.19e-02 7.06e+03 1.05e+01
  ... (remaining 5759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 7510
        1.21 -     2.42: 210
        2.42 -     3.64: 67
        3.64 -     4.85: 18
        4.85 -     6.06: 7
  Bond angle restraints: 7812
  Sorted by residual:
  angle pdb=" N   GLU A  49 "
        pdb=" CA  GLU A  49 "
        pdb=" C   GLU A  49 "
      ideal   model   delta    sigma   weight residual
     112.23  106.86    5.37 1.26e+00 6.30e-01 1.82e+01
  angle pdb=" CA  LEU A 491 "
        pdb=" C   LEU A 491 "
        pdb=" N   SER A 492 "
      ideal   model   delta    sigma   weight residual
     117.63  122.73   -5.10 1.25e+00 6.40e-01 1.66e+01
  angle pdb=" N   ASP A 668 "
        pdb=" CA  ASP A 668 "
        pdb=" C   ASP A 668 "
      ideal   model   delta    sigma   weight residual
     111.07  106.73    4.34 1.07e+00 8.73e-01 1.65e+01
  angle pdb=" N   ILE A 642 "
        pdb=" CA  ILE A 642 "
        pdb=" CB  ILE A 642 "
      ideal   model   delta    sigma   weight residual
     110.58  116.35   -5.77 1.50e+00 4.44e-01 1.48e+01
  angle pdb=" C   ASP A 668 "
        pdb=" CA  ASP A 668 "
        pdb=" CB  ASP A 668 "
      ideal   model   delta    sigma   weight residual
     110.88  104.99    5.89 1.57e+00 4.06e-01 1.41e+01
  ... (remaining 7807 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 3286
       16.84 -    33.68: 168
       33.68 -    50.51: 26
       50.51 -    67.35: 11
       67.35 -    84.19: 8
  Dihedral angle restraints: 3499
    sinusoidal: 1415
      harmonic: 2084
  Sorted by residual:
  dihedral pdb=" CA  LEU A 343 "
           pdb=" C   LEU A 343 "
           pdb=" N   MET A 344 "
           pdb=" CA  MET A 344 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.90  -17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CB  MET A 470 "
           pdb=" CG  MET A 470 "
           pdb=" SD  MET A 470 "
           pdb=" CE  MET A 470 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.11  -49.11     3      1.50e+01 4.44e-03 8.73e+00
  dihedral pdb=" CA  GLN A 186 "
           pdb=" CB  GLN A 186 "
           pdb=" CG  GLN A 186 "
           pdb=" CD  GLN A 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.88   46.12     3      1.50e+01 4.44e-03 8.28e+00
  ... (remaining 3496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 712
       0.050 -    0.100: 108
       0.100 -    0.150: 35
       0.150 -    0.201: 4
       0.201 -    0.251: 5
  Chirality restraints: 864
  Sorted by residual:
  chirality pdb=" CG  LEU A 210 "
            pdb=" CB  LEU A 210 "
            pdb=" CD1 LEU A 210 "
            pdb=" CD2 LEU A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 118 "
            pdb=" CA  VAL A 118 "
            pdb=" CG1 VAL A 118 "
            pdb=" CG2 VAL A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.86    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU A 491 "
            pdb=" CB  LEU A 491 "
            pdb=" CD1 LEU A 491 "
            pdb=" CD2 LEU A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 861 not shown)

  Planarity restraints: 1034
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 197 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.11e+00
        pdb=" C   GLN A 197 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLN A 197 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 198 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 490 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.31e+00
        pdb=" C   VAL A 490 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   VAL A 490 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 491 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 569 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   PHE A 569 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   PHE A 569 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLU A 570 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1031 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1550
        2.82 -     3.34: 5621
        3.34 -     3.86: 9547
        3.86 -     4.38: 11823
        4.38 -     4.90: 20105
  Nonbonded interactions: 48646
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 104 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   PHE A 453 "
            pdb=" OG1 THR A 457 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" OG  SER A 381 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   ASP A 426 "
            pdb=" OH  TYR A 485 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OG1 THR A 451 "
            pdb=" OE1 GLU A 486 "
     model   vdw
     2.349 3.040
  ... (remaining 48641 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.670
  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:13.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
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   0.080   5764  Z= 0.339
  Angle     :  0.581   6.059   7812  Z= 0.361
  Chirality :  0.045   0.251    864
  Planarity :  0.004   0.036   1034
  Dihedral  : 11.882  84.188   2155
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.83 %
    Favored  : 99.00 %
  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: -0.02 (0.31), residues: 721
  helix:  1.12 (0.28), residues: 352
  sheet: -1.77 (0.56), residues: 69
  loop : -0.89 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 544 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.003   0.000   ARG A 636 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  281 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6061 (mm-30)
REVERT: A  570 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6709 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 1.4417
  time to fit residues: 142.5261
Evaluate side-chains
  64 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 378 GLN
A 593 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5764  Z= 0.351
  Angle     :  0.594   7.478   7812  Z= 0.317
  Chirality :  0.046   0.145    864
  Planarity :  0.005   0.037   1034
  Dihedral  :  4.390  18.173    784
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.50 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.31), residues: 721
  helix:  1.09 (0.28), residues: 355
  sheet: -1.69 (0.57), residues: 69
  loop : -0.93 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 169 
 HIS   0.008   0.001   HIS A 648 
 PHE   0.011   0.002   PHE A 448 
 TYR   0.019   0.002   TYR A 485 
 ARG   0.005   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  281 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6115 (mm-30)
REVERT: A  629 MET cc_start: 0.8182 (ttp) cc_final: 0.7790 (ttt)
REVERT: A  669 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6646 (tt0)
  outliers start: 8
  outliers final: 1
  residues processed: 72
  average time/residue: 1.3470
  time to fit residues: 101.4565
Evaluate side-chains
  66 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0770
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 58 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5764  Z= 0.189
  Angle     :  0.488   6.365   7812  Z= 0.261
  Chirality :  0.041   0.140    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  4.096  16.702    784
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.67 %
    Favored  : 86.67 %
  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:  0.30 (0.31), residues: 721
  helix:  1.39 (0.28), residues: 358
  sheet: -1.46 (0.60), residues: 63
  loop : -0.85 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.008   0.001   PHE A 495 
 TYR   0.017   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.7748 (tp) cc_final: 0.7542 (tp)
REVERT: A  281 GLU cc_start: 0.6287 (mm-30) cc_final: 0.6047 (mm-30)
REVERT: A  623 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (tt)
REVERT: A  629 MET cc_start: 0.8100 (ttp) cc_final: 0.7759 (ttt)
REVERT: A  669 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6585 (tt0)
  outliers start: 10
  outliers final: 1
  residues processed: 78
  average time/residue: 1.1779
  time to fit residues: 96.6132
Evaluate side-chains
  69 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0770
   chunk 69 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0270
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5764  Z= 0.151
  Angle     :  0.463   5.984   7812  Z= 0.246
  Chirality :  0.041   0.141    864
  Planarity :  0.004   0.033   1034
  Dihedral  :  3.930  15.524    784
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.50 %
    Favored  : 85.50 %
  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:  0.58 (0.31), residues: 721
  helix:  1.60 (0.28), residues: 359
  sheet: -1.36 (0.62), residues: 62
  loop : -0.69 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 481 
 HIS   0.005   0.001   HIS A  44 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.005   0.000   ARG A   9 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6738 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7248 (m-10) cc_final: 0.6812 (m-80)
REVERT: A  281 GLU cc_start: 0.6262 (mm-30) cc_final: 0.6055 (mm-30)
REVERT: A  623 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5474 (tt)
REVERT: A  629 MET cc_start: 0.8071 (ttp) cc_final: 0.7849 (ttt)
REVERT: A  669 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6583 (tt0)
  outliers start: 12
  outliers final: 3
  residues processed: 74
  average time/residue: 1.1003
  time to fit residues: 85.8586
Evaluate side-chains
  68 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5764  Z= 0.200
  Angle     :  0.488   7.489   7812  Z= 0.256
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.033   1034
  Dihedral  :  3.969  15.390    784
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.83 %
    Favored  : 84.50 %
  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:  0.54 (0.31), residues: 721
  helix:  1.58 (0.28), residues: 359
  sheet: -1.33 (0.61), residues: 64
  loop : -0.73 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A    9 ARG cc_start: 0.7361 (ptt180) cc_final: 0.7030 (ptt90)
REVERT: A   97 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6785 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7273 (m-10) cc_final: 0.6820 (m-80)
REVERT: A  281 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6076 (mm-30)
REVERT: A  486 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: A  623 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5468 (tt)
REVERT: A  629 MET cc_start: 0.8073 (ttp) cc_final: 0.7855 (ttt)
REVERT: A  669 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6595 (tt0)
  outliers start: 16
  outliers final: 5
  residues processed: 76
  average time/residue: 1.1510
  time to fit residues: 92.0080
Evaluate side-chains
  70 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0060
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5764  Z= 0.195
  Angle     :  0.472   5.643   7812  Z= 0.251
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.033   1034
  Dihedral  :  3.964  15.241    784
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.83 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.31), residues: 721
  helix:  1.66 (0.28), residues: 360
  sheet: -1.19 (0.62), residues: 63
  loop : -0.75 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6880 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7242 (m-10) cc_final: 0.6796 (m-80)
REVERT: A  154 MET cc_start: 0.7614 (tpt) cc_final: 0.7324 (tpt)
REVERT: A  281 GLU cc_start: 0.6296 (mm-30) cc_final: 0.6077 (mm-30)
REVERT: A  486 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: A  623 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5435 (tt)
REVERT: A  629 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7822 (ttt)
REVERT: A  669 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6574 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 73
  average time/residue: 1.2727
  time to fit residues: 97.4751
Evaluate side-chains
  75 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0040
   chunk 38 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5764  Z= 0.163
  Angle     :  0.465   8.247   7812  Z= 0.244
  Chirality :  0.040   0.135    864
  Planarity :  0.004   0.035   1034
  Dihedral  :  3.874  14.941    784
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.50 %
    Favored  : 83.67 %
  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:  0.72 (0.32), residues: 721
  helix:  1.75 (0.28), residues: 360
  sheet: -1.13 (0.63), residues: 63
  loop : -0.71 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 481 
 HIS   0.003   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5242 (mp)
REVERT: A   97 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6881 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7240 (m-10) cc_final: 0.6798 (m-80)
REVERT: A  281 GLU cc_start: 0.6268 (mm-30) cc_final: 0.6052 (mm-30)
REVERT: A  623 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5397 (tt)
REVERT: A  629 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7811 (ttt)
REVERT: A  669 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6551 (tt0)
  outliers start: 11
  outliers final: 3
  residues processed: 71
  average time/residue: 1.1321
  time to fit residues: 84.7658
Evaluate side-chains
  70 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5764  Z= 0.183
  Angle     :  0.464   5.251   7812  Z= 0.246
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.038   1034
  Dihedral  :  3.902  15.265    784
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.17 %
    Favored  : 82.83 %
  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:  0.66 (0.32), residues: 721
  helix:  1.71 (0.28), residues: 360
  sheet: -1.30 (0.63), residues: 62
  loop : -0.74 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.001   0.000   ARG A 288 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A   12 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5274 (mp)
REVERT: A   97 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6905 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7245 (m-10) cc_final: 0.6798 (m-80)
REVERT: A  281 GLU cc_start: 0.6286 (mm-30) cc_final: 0.6058 (mm-30)
REVERT: A  486 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7046 (mm-30)
REVERT: A  623 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5416 (tt)
REVERT: A  629 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7807 (ttt)
REVERT: A  669 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6541 (tt0)
  outliers start: 12
  outliers final: 4
  residues processed: 68
  average time/residue: 1.1930
  time to fit residues: 85.3373
Evaluate side-chains
  72 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 19 optimal weight:    0.0870
   chunk 58 optimal weight:    0.0770
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5764  Z= 0.144
  Angle     :  0.449   5.796   7812  Z= 0.240
  Chirality :  0.040   0.134    864
  Planarity :  0.003   0.032   1034
  Dihedral  :  3.800  15.002    784
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.83 %
    Favored  : 82.83 %
  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 (0.32), residues: 721
  helix:  1.81 (0.28), residues: 360
  sheet: -1.15 (0.64), residues: 63
  loop : -0.65 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 481 
 HIS   0.002   0.001   HIS A 462 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.015   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 527 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A   42 ILE cc_start: 0.6786 (mp) cc_final: 0.6288 (mp)
REVERT: A  126 TYR cc_start: 0.7243 (m-10) cc_final: 0.6822 (m-80)
REVERT: A  281 GLU cc_start: 0.6266 (mm-30) cc_final: 0.6048 (mm-30)
REVERT: A  312 LYS cc_start: 0.6261 (ttmt) cc_final: 0.5997 (mtpp)
REVERT: A  465 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7534 (ttm)
REVERT: A  486 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6861 (mm-30)
REVERT: A  629 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7783 (ttt)
REVERT: A  669 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6537 (tt0)
  outliers start: 8
  outliers final: 2
  residues processed: 72
  average time/residue: 1.4198
  time to fit residues: 107.4705
Evaluate side-chains
  69 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5764  Z= 0.215
  Angle     :  0.492   6.130   7812  Z= 0.260
  Chirality :  0.042   0.137    864
  Planarity :  0.004   0.039   1034
  Dihedral  :  3.937  15.644    784
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.00 %
    Favored  : 82.83 %
  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:  0.62 (0.32), residues: 721
  helix:  1.68 (0.28), residues: 360
  sheet: -1.30 (0.64), residues: 62
  loop : -0.74 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.010   0.001   PHE A 453 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 716 

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

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

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1442 Ramachandran restraints generated.
    721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.556 
Fit side-chains
REVERT: A   97 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6938 (ttp-110)
REVERT: A  126 TYR cc_start: 0.7268 (m-10) cc_final: 0.6829 (m-80)
REVERT: A  281 GLU cc_start: 0.6307 (mm-30) cc_final: 0.6081 (mm-30)
REVERT: A  465 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7520 (ttm)
REVERT: A  486 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7336 (mm-30)
REVERT: A  629 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7778 (ttt)
REVERT: A  669 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6617 (tt0)
  outliers start: 7
  outliers final: 3
  residues processed: 67
  average time/residue: 1.2469
  time to fit residues: 87.5930
Evaluate side-chains
  70 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ARG
Chi-restraints excluded: chain A residue  422 MET
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  669 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.167750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151610 restraints weight = 5858.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.21
r_work: 0.3580 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5764  Z= 0.191
  Angle     :  0.487   7.002   7812  Z= 0.256
  Chirality :  0.041   0.136    864
  Planarity :  0.004   0.037   1034
  Dihedral  :  3.932  15.774    784
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.17 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.32), residues: 721
  helix:  1.68 (0.28), residues: 360
  sheet: -1.25 (0.65), residues: 62
  loop : -0.74 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.009   0.001   PHE A 495 
 TYR   0.016   0.001   TYR A 485 
 ARG   0.002   0.000   ARG A 288 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2344.03 seconds
wall clock time: 41 minutes 50.29 seconds (2510.29 seconds total)