Starting phenix.real_space_refine
on Fri Feb 14 08:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pmw_13542/02_2025/7pmw_13542.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    3298      2.51       5
     N     806      2.21       5
     O     894      1.98       5
     H    5123      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10153
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 10120
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 29, 'TRANS': 611}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 1}
  Time building chain proxies: 5.62, per 1000 atoms: 0.55
  Number of scatterers: 10153
  At special positions: 0
  Unit cell: (82.41, 91.12, 120.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O     894      8.00
     N     806      7.00
     C    3298      6.00
     H    5123      1.00
    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: 2.90
  Conformation dependent library (CDL) restraints added in 715.5 milliseconds
  

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1202

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 5 sheets defined
      60.8% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 42
      removed outlier: 4.233A  pdb=" N   ILE A  16 " --> pdb=" O   TYR A  12 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET A  33 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG A  34 " --> pdb=" O   TYR A  30 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA A  35 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.622A  pdb=" N   TYR A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 3.905A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 108
      removed outlier: 3.630A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 149
      removed outlier: 3.784A  pdb=" N   SER A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLY A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LYS A 140 " --> pdb=" O   THR A 136 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
      removed outlier: 3.681A  pdb=" N   SER A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 148 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 181
      removed outlier: 3.718A  pdb=" N   ASN A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 219
      Proline residue:  A 205  - end of helix
      removed outlier: 3.712A  pdb=" N   MET A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 222
      No H-bonds generated for 'chain 'A' and resid 220 through 222'
    Processing helix  chain 'A' and resid 231 through 249
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 3.661A  pdb=" N   ALA A 265 " --> pdb=" O   TRP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 287
      removed outlier: 3.775A  pdb=" N   LEU A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 298
      removed outlier: 4.126A  pdb=" N   TRP A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 296 " --> pdb=" O   MET A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 4.206A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A 300 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   THR A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   THR A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 326 through 343
      removed outlier: 4.034A  pdb=" N   ALA A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
      removed outlier: 3.557A  pdb=" N   ASP A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
    Processing helix  chain 'A' and resid 356 through 383
      removed outlier: 3.745A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 367 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 368 " --> pdb=" O   GLY A 364 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A 374 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP A 383 " --> pdb=" O   GLN A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.664A  pdb=" N   GLU A 485 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 582
      No H-bonds generated for 'chain 'A' and resid 580 through 582'
    Processing helix  chain 'A' and resid 583 through 610
      removed outlier: 4.698A  pdb=" N   GLN A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL A 597 " --> pdb=" O   CYS A 593 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA A 610 " --> pdb=" O   SER A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 637
      removed outlier: 3.768A  pdb=" N   LEU A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A 619 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A 626 " --> pdb=" O   TRP A 622 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 627 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 628 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 632 " --> pdb=" O   VAL A 628 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 633 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 651
      removed outlier: 4.067A  pdb=" N   ALA A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 668
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 5.626A  pdb=" N   TYR A 672 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 674 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.199A  pdb=" N   ALA A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423
      removed outlier: 6.845A  pdb=" N   HIS A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418
    Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521
      removed outlier: 6.614A  pdb=" N   GLY A 487 " --> pdb=" O   TYR A 554 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   TYR A 556 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ARG A 489 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   VAL A 558 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA A 553 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 510
      removed outlier: 6.303A  pdb=" N   ILE A 498 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    747 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: 3.62

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5113
        1.03 -     1.23: 12
        1.23 -     1.42: 2135
        1.42 -     1.61: 2957
        1.61 -     1.81: 54
  Bond restraints: 10271
  Sorted by residual:
  bond pdb=" N   ASN A 329 "
       pdb=" CA  ASN A 329 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.80e+00
  bond pdb=" N   ASN A 329 "
       pdb=" H   ASN A 329 "
    ideal  model  delta    sigma   weight residual
    0.860  0.914 -0.054 2.00e-02 2.50e+03 7.25e+00
  bond pdb=" C   ASN A 329 "
       pdb=" O   ASN A 329 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.19e-02 7.06e+03 4.39e+00
  bond pdb=" C   ASN A 329 "
       pdb=" N   ALA A 330 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.025 1.36e-02 5.41e+03 3.25e+00
  bond pdb=" ND2 ASN A 329 "
       pdb="HD22 ASN A 329 "
    ideal  model  delta    sigma   weight residual
    0.860  0.885 -0.025 2.00e-02 2.50e+03 1.53e+00
  ... (remaining 10266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.02: 18584
        7.02 -    14.05: 2
       14.05 -    21.07: 0
       21.07 -    28.09: 0
       28.09 -    35.11: 6
  Bond angle restraints: 18592
  Sorted by residual:
  angle pdb=" C   LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   73.89   35.11 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" C   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     109.00   74.26   34.74 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" N   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     110.00   75.29   34.71 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" N   LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     110.00   75.86   34.14 3.00e+00 1.11e-01 1.30e+02
  angle pdb=" CB  LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   75.27   33.73 3.00e+00 1.11e-01 1.26e+02
  ... (remaining 18587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4572
       17.96 -    35.92: 191
       35.92 -    53.88: 65
       53.88 -    71.84: 26
       71.84 -    89.80: 5
  Dihedral angle restraints: 4859
    sinusoidal: 2592
      harmonic: 2267
  Sorted by residual:
  dihedral pdb=" C   LEU A  51 "
           pdb=" N   LEU A  51 "
           pdb=" CA  LEU A  51 "
           pdb=" CB  LEU A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.99    9.39     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" C   GLN A 609 "
           pdb=" N   GLN A 609 "
           pdb=" CA  GLN A 609 "
           pdb=" CB  GLN A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.75    9.15     0      2.50e+00 1.60e-01 1.34e+01
  dihedral pdb=" C   ASN A 329 "
           pdb=" N   ASN A 329 "
           pdb=" CA  ASN A 329 "
           pdb=" CB  ASN A 329 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.57   -9.03     0      2.50e+00 1.60e-01 1.30e+01
  ... (remaining 4856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 758
       0.078 -    0.156: 49
       0.156 -    0.234: 0
       0.234 -    0.311: 0
       0.311 -    0.389: 2
  Chirality restraints: 809
  Sorted by residual:
  chirality pdb=" CA  GLN A 609 "
            pdb=" N   GLN A 609 "
            pdb=" C   GLN A 609 "
            pdb=" CB  GLN A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  LEU A  51 "
            pdb=" N   LEU A  51 "
            pdb=" C   LEU A  51 "
            pdb=" CB  LEU A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  ASN A 329 "
            pdb=" N   ASN A 329 "
            pdb=" C   ASN A 329 "
            pdb=" CB  ASN A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 806 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 329 "    0.107 2.00e-02 2.50e+03   1.13e-01 1.93e+02
        pdb=" CG  ASN A 329 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 329 "   -0.101 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 329 "    0.004 2.00e-02 2.50e+03
        pdb="HD21 ASN A 329 "    0.168 2.00e-02 2.50e+03
        pdb="HD22 ASN A 329 "   -0.165 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 535 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.28e+00
        pdb=" N   PRO A 536 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 536 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 536 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 585 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO A 586 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 586 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 586 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 70
        1.95 -     2.61: 11824
        2.61 -     3.28: 30968
        3.28 -     3.94: 36170
        3.94 -     4.60: 57202
  Nonbonded interactions: 136234
  Sorted by model distance:
  nonbonded pdb="HD22 ASN A 171 "
            pdb="HD13 ILE A 333 "
     model   vdw
     1.291 2.270
  nonbonded pdb="HD21 ASN A 171 "
            pdb="HG21 ILE A 333 "
     model   vdw
     1.293 2.270
  nonbonded pdb=" HB3 HIS A  57 "
            pdb="HD21 ASN A 630 "
     model   vdw
     1.554 2.270
  nonbonded pdb=" H   ARG A 258 "
            pdb=" OD2 ASP A 263 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" O   GLY A 419 "
            pdb=" HG  SER A 422 "
     model   vdw
     1.615 2.450
  ... (remaining 136229 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.400
  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:             0.180
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.780
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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      :  0.002   0.034   5148  Z= 0.124
  Angle     :  0.467   9.658   6989  Z= 0.259
  Chirality :  0.043   0.389    809
  Planarity :  0.003   0.028    873
  Dihedral  :  9.249  54.339   1835
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  3.64 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.17 %
  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:  0.56 (0.35), residues: 633
  helix:  0.74 (0.31), residues: 297
  sheet:  1.33 (0.64), residues: 71
  loop : -0.19 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 469 
 PHE   0.005   0.001   PHE A 520 
 TYR   0.004   0.001   TYR A  56 
 ARG   0.002   0.000   ARG A  34 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.9182 (p) cc_final: 0.8757 (t)
REVERT: A  198 TYR cc_start: 0.7554 (m-80) cc_final: 0.7248 (m-80)
REVERT: A  292 MET cc_start: 0.8132 (tpt) cc_final: 0.7855 (tpp)
REVERT: A  306 LEU cc_start: 0.8622 (tp) cc_final: 0.8383 (mt)
REVERT: A  312 SER cc_start: 0.7470 (p) cc_final: 0.7244 (t)
REVERT: A  617 VAL cc_start: 0.9018 (t) cc_final: 0.8758 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 142
  average time/residue: 0.3856
  time to fit residues: 69.4310
Evaluate side-chains
  99 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 37 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 393 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.121005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.100323 restraints weight = 42572.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.103655 restraints weight = 24144.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.106012 restraints weight = 16678.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5148  Z= 0.215
  Angle     :  0.602   5.285   6989  Z= 0.334
  Chirality :  0.047   0.403    809
  Planarity :  0.005   0.030    873
  Dihedral  :  4.385  16.390    680
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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 (0.34), residues: 633
  helix:  0.73 (0.28), residues: 312
  sheet:  0.87 (0.63), residues: 67
  loop : -0.11 (0.43), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.017   0.001   PHE A 248 
 TYR   0.019   0.001   TYR A 588 
 ARG   0.008   0.001   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.8313 (m) cc_final: 0.8105 (t)
REVERT: A   95 GLN cc_start: 0.8594 (mt0) cc_final: 0.8060 (tt0)
REVERT: A  198 TYR cc_start: 0.7524 (m-80) cc_final: 0.7187 (m-80)
REVERT: A  312 SER cc_start: 0.7150 (p) cc_final: 0.6846 (t)
REVERT: A  407 MET cc_start: 0.7791 (mmp) cc_final: 0.7270 (mmt)
REVERT: A  581 MET cc_start: 0.8345 (ttm) cc_final: 0.8133 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.3375
  time to fit residues: 49.1273
Evaluate side-chains
  83 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    0.0470
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.8882

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

Flipped N/Q/H residues before XYZ refinement:
A 609 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.119975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.098274 restraints weight = 43473.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.101828 restraints weight = 24424.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.104321 restraints weight = 16737.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5148  Z= 0.212
  Angle     :  0.540   5.247   6989  Z= 0.301
  Chirality :  0.045   0.383    809
  Planarity :  0.004   0.036    873
  Dihedral  :  4.423  20.448    680
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.29 (0.33), residues: 633
  helix:  0.65 (0.28), residues: 313
  sheet:  0.47 (0.63), residues: 67
  loop : -0.33 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 260 
 PHE   0.012   0.001   PHE A 162 
 TYR   0.012   0.001   TYR A 167 
 ARG   0.004   0.001   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8551 (mt0) cc_final: 0.8065 (tt0)
REVERT: A  312 SER cc_start: 0.7064 (p) cc_final: 0.6841 (t)
REVERT: A  407 MET cc_start: 0.7809 (mmp) cc_final: 0.7348 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.3263
  time to fit residues: 40.8235
Evaluate side-chains
  85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 42 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.121788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.100641 restraints weight = 43096.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.104207 restraints weight = 23819.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.106653 restraints weight = 16361.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5148  Z= 0.161
  Angle     :  0.513   6.080   6989  Z= 0.275
  Chirality :  0.044   0.393    809
  Planarity :  0.004   0.064    873
  Dihedral  :  4.371  21.191    680
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.52 (0.34), residues: 633
  helix:  0.92 (0.28), residues: 312
  sheet:  0.46 (0.62), residues: 67
  loop : -0.28 (0.43), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  77 
 HIS   0.004   0.001   HIS A 260 
 PHE   0.015   0.001   PHE A  41 
 TYR   0.015   0.001   TYR A 588 
 ARG   0.006   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8444 (mt0) cc_final: 0.8042 (tt0)
REVERT: A  198 TYR cc_start: 0.7534 (m-80) cc_final: 0.7166 (m-80)
REVERT: A  312 SER cc_start: 0.6858 (p) cc_final: 0.6620 (t)
REVERT: A  407 MET cc_start: 0.7738 (mmp) cc_final: 0.7265 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.3217
  time to fit residues: 41.9573
Evaluate side-chains
  85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.119229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097336 restraints weight = 43711.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.100657 restraints weight = 25318.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.102998 restraints weight = 17820.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5148  Z= 0.297
  Angle     :  0.552   5.536   6989  Z= 0.309
  Chirality :  0.045   0.436    809
  Planarity :  0.005   0.055    873
  Dihedral  :  4.515  20.685    680
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.33 (0.33), residues: 633
  helix:  0.79 (0.28), residues: 313
  sheet:  0.30 (0.62), residues: 67
  loop : -0.40 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 260 
 PHE   0.015   0.001   PHE A  41 
 TYR   0.013   0.001   TYR A 167 
 ARG   0.003   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8492 (mt0) cc_final: 0.8076 (tt0)
REVERT: A  312 SER cc_start: 0.7113 (p) cc_final: 0.6904 (t)
REVERT: A  407 MET cc_start: 0.7739 (mmp) cc_final: 0.7318 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3283
  time to fit residues: 42.0807
Evaluate side-chains
  85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0870
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.121280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.100219 restraints weight = 43541.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.103893 restraints weight = 24045.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.106410 restraints weight = 16198.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5148  Z= 0.156
  Angle     :  0.507   5.480   6989  Z= 0.271
  Chirality :  0.044   0.421    809
  Planarity :  0.004   0.045    873
  Dihedral  :  4.428  21.755    680
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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:  0.60 (0.34), residues: 633
  helix:  1.06 (0.29), residues: 314
  sheet:  0.41 (0.63), residues: 67
  loop : -0.35 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 622 
 HIS   0.010   0.001   HIS A 260 
 PHE   0.013   0.001   PHE A  41 
 TYR   0.012   0.001   TYR A 588 
 ARG   0.003   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7693 (mmp) cc_final: 0.7262 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3359
  time to fit residues: 43.1914
Evaluate side-chains
  83 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.117470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.095926 restraints weight = 44516.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.099397 restraints weight = 24621.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.101804 restraints weight = 16670.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5148  Z= 0.321
  Angle     :  0.567   5.515   6989  Z= 0.318
  Chirality :  0.045   0.391    809
  Planarity :  0.005   0.051    873
  Dihedral  :  4.656  20.766    680
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  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:  0.14 (0.33), residues: 633
  helix:  0.61 (0.28), residues: 315
  sheet:  0.22 (0.62), residues: 67
  loop : -0.47 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.001   HIS A 260 
 PHE   0.014   0.002   PHE A 162 
 TYR   0.016   0.001   TYR A 167 
 ARG   0.004   0.001   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7731 (mmp) cc_final: 0.7459 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.3701
  time to fit residues: 45.4660
Evaluate side-chains
  83 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 50 optimal weight:    7.9990
   chunk 8 optimal weight:    0.4980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.119753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.098617 restraints weight = 43529.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.102385 restraints weight = 23327.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.104919 restraints weight = 15399.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5148  Z= 0.153
  Angle     :  0.497   5.616   6989  Z= 0.267
  Chirality :  0.044   0.390    809
  Planarity :  0.004   0.041    873
  Dihedral  :  4.458  19.297    680
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.56 (0.34), residues: 633
  helix:  0.95 (0.29), residues: 318
  sheet:  0.46 (0.62), residues: 67
  loop : -0.29 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.012   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7738 (mmp) cc_final: 0.7485 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.3022
  time to fit residues: 36.8339
Evaluate side-chains
  79 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0020
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 609 GLN
A 674 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.120566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.098785 restraints weight = 44441.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.102291 restraints weight = 25387.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.104749 restraints weight = 17499.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5148  Z= 0.168
  Angle     :  0.500   5.273   6989  Z= 0.269
  Chirality :  0.043   0.383    809
  Planarity :  0.004   0.040    873
  Dihedral  :  4.434  18.943    680
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.36 %
    Favored  : 99.45 %
  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:  0.60 (0.34), residues: 633
  helix:  1.09 (0.29), residues: 315
  sheet:  0.46 (0.63), residues: 67
  loop : -0.41 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.011   0.001   PHE A 166 
 TYR   0.010   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A  27 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7691 (mmp) cc_final: 0.7447 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 87
  average time/residue: 0.2996
  time to fit residues: 35.4911
Evaluate side-chains
  79 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.119462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.098151 restraints weight = 43917.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.101398 restraints weight = 25778.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.103782 restraints weight = 18133.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5148  Z= 0.266
  Angle     :  0.529   5.231   6989  Z= 0.293
  Chirality :  0.044   0.379    809
  Planarity :  0.004   0.042    873
  Dihedral  :  4.523  19.140    680
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.38 (0.33), residues: 633
  helix:  0.82 (0.29), residues: 320
  sheet:  0.39 (0.63), residues: 67
  loop : -0.43 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.019   0.001   PHE A 372 
 TYR   0.016   0.001   TYR A 588 
 ARG   0.002   0.000   ARG A 303 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 LEU cc_start: 0.9080 (mt) cc_final: 0.8831 (mm)
REVERT: A  407 MET cc_start: 0.7652 (mmp) cc_final: 0.7422 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.3124
  time to fit residues: 35.3294
Evaluate side-chains
  79 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.118192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.096170 restraints weight = 43970.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.099328 restraints weight = 26243.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.101509 restraints weight = 18602.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5148  Z= 0.324
  Angle     :  0.578   5.043   6989  Z= 0.323
  Chirality :  0.045   0.384    809
  Planarity :  0.005   0.042    873
  Dihedral  :  4.729  19.141    680
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.09 (0.34), residues: 633
  helix:  0.60 (0.28), residues: 313
  sheet:  0.28 (0.63), residues: 67
  loop : -0.56 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.001   HIS A 260 
 PHE   0.030   0.002   PHE A 372 
 TYR   0.018   0.002   TYR A 167 
 ARG   0.003   0.001   ARG A  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3538.94 seconds
wall clock time: 63 minutes 18.00 seconds (3798.00 seconds total)