Starting phenix.real_space_refine
on Thu May  1 01:09:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw3_38729/05_2025/8xw3_38729.cif"
  }
  resolution = 3.63
  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=   0.006 sd=   0.062
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      48      5.16       5
     C    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.91, per 1000 atoms: 0.98
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (91.785, 142.425, 99.17, 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      48     16.00
     O    1708      8.00
     N    1650      7.00
     C    6744      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: 2.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 2 sheets defined
      75.8% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.571A  pdb=" N   GLN A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.880A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.088A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 315
      removed outlier: 3.669A  pdb=" N   ASN A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 360 through 364
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.693A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 4.411A  pdb=" N   ILE A 425 " --> pdb=" O   MET A 421 " (cutoff:3.500A)
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 475
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 512
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 3.944A  pdb=" N   ALA A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLY A 527 " --> pdb=" O   ASP A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.615A  pdb=" N   ILE A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 647
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 3.978A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.466A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 31
      removed outlier: 3.571A  pdb=" N   GLN B  31 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.880A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.088A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 315
      removed outlier: 3.669A  pdb=" N   ASN B 314 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 338
    Processing helix  chain 'B' and resid 360 through 364
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'B' and resid 389 through 400
      removed outlier: 3.693A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 438
      removed outlier: 4.411A  pdb=" N   ILE B 425 " --> pdb=" O   MET B 421 " (cutoff:3.500A)
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 512
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 512 through 532
      removed outlier: 3.945A  pdb=" N   ALA B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLY B 527 " --> pdb=" O   ASP B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.616A  pdb=" N   ILE B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 647
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
      removed outlier: 3.979A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.466A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.779A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.779A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    697 hydrogen bonds defined for protein.
    2067 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: 2.97

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3011
        1.34 -     1.46: 1764
        1.46 -     1.58: 5577
        1.58 -     1.70: 0
        1.70 -     1.81: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" CB  VAL B 476 "
       pdb=" CG1 VAL B 476 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.52e+00
  bond pdb=" CB  VAL A 476 "
       pdb=" CG1 VAL A 476 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.48e+00
  bond pdb=" CG  LEU B 579 "
       pdb=" CD2 LEU B 579 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.79e+00
  bond pdb=" CG  LEU A 579 "
       pdb=" CD2 LEU A 579 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CA  GLU A 452 "
       pdb=" CB  GLU A 452 "
    ideal  model  delta    sigma   weight residual
    1.528  1.510  0.017 1.39e-02 5.18e+03 1.56e+00
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 13595
        1.51 -     3.01: 459
        3.01 -     4.52: 90
        4.52 -     6.02: 46
        6.02 -     7.53: 10
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" C   PHE B 451 "
        pdb=" N   GLU B 452 "
        pdb=" CA  GLU B 452 "
      ideal   model   delta    sigma   weight residual
     123.11  117.16    5.95 1.42e+00 4.96e-01 1.76e+01
  angle pdb=" C   PHE A 451 "
        pdb=" N   GLU A 452 "
        pdb=" CA  GLU A 452 "
      ideal   model   delta    sigma   weight residual
     123.11  117.19    5.92 1.42e+00 4.96e-01 1.74e+01
  angle pdb=" CA  GLU B 452 "
        pdb=" CB  GLU B 452 "
        pdb=" CG  GLU B 452 "
      ideal   model   delta    sigma   weight residual
     114.10  107.63    6.47 2.00e+00 2.50e-01 1.05e+01
  angle pdb=" CA  GLU A 452 "
        pdb=" CB  GLU A 452 "
        pdb=" CG  GLU A 452 "
      ideal   model   delta    sigma   weight residual
     114.10  107.64    6.46 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" N   TRP A  42 "
        pdb=" CA  TRP A  42 "
        pdb=" C   TRP A  42 "
      ideal   model   delta    sigma   weight residual
     113.72  109.33    4.39 1.52e+00 4.33e-01 8.35e+00
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 5510
       16.44 -    32.88: 490
       32.88 -    49.33: 102
       49.33 -    65.77: 16
       65.77 -    82.21: 10
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  GLU B 452 "
           pdb=" C   GLU B 452 "
           pdb=" N   GLY B 453 "
           pdb=" CA  GLY B 453 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.49  -23.51     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  GLU A 452 "
           pdb=" C   GLU A 452 "
           pdb=" N   GLY A 453 "
           pdb=" CA  GLY A 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.50  -23.50     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  ASN A 475 "
           pdb=" C   ASN A 475 "
           pdb=" N   VAL A 476 "
           pdb=" CA  VAL A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.34  -21.66     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 795
       0.026 -    0.052: 470
       0.052 -    0.078: 187
       0.078 -    0.103: 99
       0.103 -    0.129: 53
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  THR A 455 "
            pdb=" N   THR A 455 "
            pdb=" C   THR A 455 "
            pdb=" CB  THR A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  PRO B  77 "
            pdb=" N   PRO B  77 "
            pdb=" C   PRO B  77 "
            pdb=" CB  PRO B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  THR B 455 "
            pdb=" N   THR B 455 "
            pdb=" C   THR B 455 "
            pdb=" CB  THR B 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 677 "    0.033 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO B 678 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 678 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 678 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 677 "   -0.033 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A 678 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 678 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 678 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 472 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   ASN B 472 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN B 472 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B 473 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 101
        2.65 -     3.21: 9992
        3.21 -     3.77: 16258
        3.77 -     4.34: 20568
        4.34 -     4.90: 34305
  Nonbonded interactions: 81224
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 354 "
            pdb=" OH  TYR B 712 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" NH2 ARG A 198 "
            pdb=" OD2 ASP A 200 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG B 198 "
            pdb=" OD2 ASP B 200 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   GLU A 195 "
            pdb=" NZ  LYS A 691 "
     model   vdw
     2.293 3.120
  ... (remaining 81219 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     30.020
  Find NCS groups from input model:        0.180
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
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   0.052  10440  Z= 0.226
  Angle     :  0.728   7.529  14200  Z= 0.399
  Chirality :  0.044   0.129   1604
  Planarity :  0.005   0.049   1762
  Dihedral  : 13.288  82.211   3696
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.24), residues: 1248
  helix:  2.11 (0.17), residues: 868
  sheet: -0.96 (0.85), residues: 36
  loop : -1.74 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 525 
 HIS   0.004   0.001   HIS B 542 
 PHE   0.022   0.002   PHE A 420 
 TYR   0.016   0.002   TYR A 468 
 ARG   0.007   0.001   ARG B 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08028 (  697)
  hydrogen bonds       : angle       4.51165 ( 2067)
  covalent geometry    : bond        0.00521 (10440)
  covalent geometry    : angle       0.72755 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.164 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7783 (m-30) cc_final: 0.7546 (m-30)
REVERT: A  521 MET cc_start: 0.8796 (tpp) cc_final: 0.8593 (tpp)
REVERT: B  395 PHE cc_start: 0.8530 (t80) cc_final: 0.8217 (t80)
REVERT: B  525 TRP cc_start: 0.8991 (m-10) cc_final: 0.8661 (m-10)
REVERT: B  536 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7352 (mmtt)
REVERT: B  613 TYR cc_start: 0.7954 (m-10) cc_final: 0.7747 (m-10)
REVERT: B  672 CYS cc_start: 0.9031 (m) cc_final: 0.8709 (m)
REVERT: B  689 MET cc_start: 0.9224 (tpt) cc_final: 0.8994 (tpt)
REVERT: B  699 GLU cc_start: 0.8354 (mp0) cc_final: 0.8003 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1764
  time to fit residues: 57.1714
Evaluate side-chains
  171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 397 GLN
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.087788 restraints weight = 19751.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.090440 restraints weight = 10696.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.092149 restraints weight = 7374.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10440  Z= 0.138
  Angle     :  0.603   6.791  14200  Z= 0.302
  Chirality :  0.042   0.164   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.261  18.959   1360
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  7.94 %
    Favored  : 90.36 %
  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:  1.73 (0.25), residues: 1248
  helix:  2.21 (0.17), residues: 872
  sheet: -0.33 (0.92), residues: 30
  loop : -1.60 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 624 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.020   0.001   PHE A 471 
 TYR   0.015   0.001   TYR A 468 
 ARG   0.004   0.000   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  697)
  hydrogen bonds       : angle       4.23456 ( 2067)
  covalent geometry    : bond        0.00328 (10440)
  covalent geometry    : angle       0.60272 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.7998 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  521 MET cc_start: 0.8870 (tpp) cc_final: 0.8617 (tpp)
REVERT: B  200 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8068 (p0)
REVERT: B  395 PHE cc_start: 0.8482 (t80) cc_final: 0.8164 (t80)
REVERT: B  511 MET cc_start: 0.7023 (mmm) cc_final: 0.6637 (mmm)
REVERT: B  521 MET cc_start: 0.8836 (tpp) cc_final: 0.8630 (tpp)
REVERT: B  540 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8118 (tmm)
REVERT: B  661 LEU cc_start: 0.8925 (mt) cc_final: 0.8698 (mt)
REVERT: B  672 CYS cc_start: 0.9052 (m) cc_final: 0.8629 (m)
REVERT: B  677 GLU cc_start: 0.8026 (tt0) cc_final: 0.7782 (tt0)
REVERT: B  689 MET cc_start: 0.9210 (tpt) cc_final: 0.9000 (tpt)
REVERT: B  699 GLU cc_start: 0.8507 (mp0) cc_final: 0.8199 (mp0)
  outliers start: 18
  outliers final: 7
  residues processed: 195
  average time/residue: 0.1813
  time to fit residues: 53.0973
Evaluate side-chains
  177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0170
   chunk 22 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 397 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.088801 restraints weight = 19965.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.091523 restraints weight = 10733.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.093282 restraints weight = 7375.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  10440  Z= 0.124
  Angle     :  0.588  13.016  14200  Z= 0.288
  Chirality :  0.041   0.160   1604
  Planarity :  0.004   0.057   1762
  Dihedral  :  4.078  17.865   1360
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.49 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.25), residues: 1248
  helix:  2.22 (0.17), residues: 874
  sheet:  0.35 (0.96), residues: 36
  loop : -1.70 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 624 
 HIS   0.002   0.000   HIS A  90 
 PHE   0.021   0.001   PHE A 471 
 TYR   0.019   0.001   TYR A 368 
 ARG   0.008   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  697)
  hydrogen bonds       : angle       4.17187 ( 2067)
  covalent geometry    : bond        0.00290 (10440)
  covalent geometry    : angle       0.58813 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 1.246 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7957 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  689 MET cc_start: 0.9147 (tpt) cc_final: 0.8906 (tpp)
REVERT: B  164 VAL cc_start: 0.9182 (t) cc_final: 0.8932 (p)
REVERT: B  383 PHE cc_start: 0.8808 (t80) cc_final: 0.8596 (t80)
REVERT: B  395 PHE cc_start: 0.8459 (t80) cc_final: 0.8167 (t80)
REVERT: B  470 ILE cc_start: 0.9004 (tp) cc_final: 0.8600 (tt)
REVERT: B  511 MET cc_start: 0.7091 (mmm) cc_final: 0.6661 (mmm)
REVERT: B  672 CYS cc_start: 0.9074 (m) cc_final: 0.8590 (m)
REVERT: B  677 GLU cc_start: 0.8026 (tt0) cc_final: 0.7773 (tt0)
REVERT: B  689 MET cc_start: 0.9195 (tpt) cc_final: 0.8980 (tpt)
  outliers start: 25
  outliers final: 15
  residues processed: 185
  average time/residue: 0.1819
  time to fit residues: 51.6372
Evaluate side-chains
  180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.114729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.088225 restraints weight = 19759.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.090884 restraints weight = 10768.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.092596 restraints weight = 7464.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10440  Z= 0.132
  Angle     :  0.576  10.070  14200  Z= 0.286
  Chirality :  0.041   0.165   1604
  Planarity :  0.004   0.057   1762
  Dihedral  :  3.978  17.425   1360
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.87 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.25), residues: 1248
  helix:  2.24 (0.17), residues: 874
  sheet:  0.09 (0.88), residues: 46
  loop : -1.85 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.019   0.001   PHE A 471 
 TYR   0.016   0.001   TYR A 181 
 ARG   0.007   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  697)
  hydrogen bonds       : angle       4.12392 ( 2067)
  covalent geometry    : bond        0.00317 (10440)
  covalent geometry    : angle       0.57600 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7904 (m-30) cc_final: 0.7590 (m-30)
REVERT: A  448 MET cc_start: 0.7331 (ttm) cc_final: 0.6687 (tpt)
REVERT: A  470 ILE cc_start: 0.9069 (tp) cc_final: 0.8866 (tp)
REVERT: A  677 GLU cc_start: 0.8136 (tt0) cc_final: 0.7850 (mt-10)
REVERT: A  689 MET cc_start: 0.9168 (tpt) cc_final: 0.8929 (tpp)
REVERT: B  383 PHE cc_start: 0.8782 (t80) cc_final: 0.8507 (t80)
REVERT: B  387 PHE cc_start: 0.8428 (t80) cc_final: 0.8115 (t80)
REVERT: B  395 PHE cc_start: 0.8503 (t80) cc_final: 0.8234 (t80)
REVERT: B  521 MET cc_start: 0.8864 (tpp) cc_final: 0.8170 (mmt)
REVERT: B  525 TRP cc_start: 0.8853 (m-10) cc_final: 0.8496 (m-10)
REVERT: B  531 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7803 (tm-30)
REVERT: B  661 LEU cc_start: 0.8900 (mt) cc_final: 0.8695 (mt)
REVERT: B  672 CYS cc_start: 0.9084 (m) cc_final: 0.8585 (m)
REVERT: B  677 GLU cc_start: 0.8049 (tt0) cc_final: 0.7772 (tt0)
  outliers start: 27
  outliers final: 20
  residues processed: 191
  average time/residue: 0.1665
  time to fit residues: 49.5903
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 111 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.112903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.086163 restraints weight = 19873.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088747 restraints weight = 10941.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.090311 restraints weight = 7648.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10440  Z= 0.154
  Angle     :  0.606   9.465  14200  Z= 0.298
  Chirality :  0.042   0.172   1604
  Planarity :  0.005   0.057   1762
  Dihedral  :  4.000  18.632   1360
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.00 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.25), residues: 1248
  helix:  2.25 (0.17), residues: 874
  sheet:  0.00 (0.85), residues: 46
  loop : -1.86 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 624 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.018   0.001   PHE A 577 
 TYR   0.018   0.001   TYR B 181 
 ARG   0.007   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  697)
  hydrogen bonds       : angle       4.09521 ( 2067)
  covalent geometry    : bond        0.00377 (10440)
  covalent geometry    : angle       0.60594 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 1.256 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7959 (m-30) cc_final: 0.7651 (m-30)
REVERT: A   30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8629 (mm)
REVERT: A   93 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8656 (tt)
REVERT: A  320 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8495 (mpp)
REVERT: A  448 MET cc_start: 0.7301 (ttm) cc_final: 0.6719 (tpt)
REVERT: A  470 ILE cc_start: 0.8976 (tp) cc_final: 0.8765 (tp)
REVERT: A  689 MET cc_start: 0.9178 (tpt) cc_final: 0.8939 (tpp)
REVERT: B  383 PHE cc_start: 0.8797 (t80) cc_final: 0.8526 (t80)
REVERT: B  387 PHE cc_start: 0.8497 (t80) cc_final: 0.8120 (t80)
REVERT: B  395 PHE cc_start: 0.8507 (t80) cc_final: 0.8212 (t80)
REVERT: B  448 MET cc_start: 0.7626 (ttp) cc_final: 0.7012 (tpt)
REVERT: B  521 MET cc_start: 0.8995 (tpp) cc_final: 0.8315 (tpp)
REVERT: B  525 TRP cc_start: 0.8884 (m-10) cc_final: 0.8475 (m-10)
REVERT: B  531 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: B  540 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8176 (tmm)
REVERT: B  672 CYS cc_start: 0.9103 (m) cc_final: 0.8582 (m)
REVERT: B  677 GLU cc_start: 0.8113 (tt0) cc_final: 0.7848 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 181
  average time/residue: 0.1667
  time to fit residues: 47.3298
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0040
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.114328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.087227 restraints weight = 19844.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.090039 restraints weight = 10450.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.091837 restraints weight = 7120.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10440  Z= 0.123
  Angle     :  0.578   9.298  14200  Z= 0.285
  Chirality :  0.041   0.179   1604
  Planarity :  0.004   0.056   1762
  Dihedral  :  3.944  17.993   1360
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.95 %
    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:  1.74 (0.25), residues: 1248
  helix:  2.24 (0.17), residues: 876
  sheet: -0.01 (0.84), residues: 46
  loop : -1.83 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 624 
 HIS   0.003   0.000   HIS B 379 
 PHE   0.016   0.001   PHE A 395 
 TYR   0.013   0.001   TYR B 181 
 ARG   0.006   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  697)
  hydrogen bonds       : angle       4.10113 ( 2067)
  covalent geometry    : bond        0.00291 (10440)
  covalent geometry    : angle       0.57844 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.7949 (m-30) cc_final: 0.7731 (m-30)
REVERT: A   30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8664 (mm)
REVERT: A   93 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8436 (tt)
REVERT: A  657 PHE cc_start: 0.8591 (m-80) cc_final: 0.8381 (m-10)
REVERT: A  677 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7830 (mt-10)
REVERT: A  689 MET cc_start: 0.9142 (tpt) cc_final: 0.8890 (tpp)
REVERT: B  164 VAL cc_start: 0.9182 (t) cc_final: 0.8940 (p)
REVERT: B  383 PHE cc_start: 0.8826 (t80) cc_final: 0.8549 (t80)
REVERT: B  387 PHE cc_start: 0.8444 (t80) cc_final: 0.8061 (t80)
REVERT: B  395 PHE cc_start: 0.8447 (t80) cc_final: 0.8165 (t80)
REVERT: B  448 MET cc_start: 0.7613 (ttp) cc_final: 0.6480 (tpt)
REVERT: B  521 MET cc_start: 0.9045 (tpp) cc_final: 0.8285 (tpp)
REVERT: B  525 TRP cc_start: 0.8820 (m-10) cc_final: 0.8450 (m-10)
REVERT: B  531 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: B  540 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8224 (tmm)
REVERT: B  575 LEU cc_start: 0.8994 (tt) cc_final: 0.8729 (tt)
REVERT: B  677 GLU cc_start: 0.8118 (tt0) cc_final: 0.7865 (tt0)
  outliers start: 27
  outliers final: 17
  residues processed: 183
  average time/residue: 0.1707
  time to fit residues: 48.8405
Evaluate side-chains
  185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 123 optimal weight:    0.7980
   chunk 120 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0370
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7660

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.114552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.087793 restraints weight = 20067.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.090465 restraints weight = 10964.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.092167 restraints weight = 7607.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10440  Z= 0.125
  Angle     :  0.594  14.053  14200  Z= 0.289
  Chirality :  0.041   0.180   1604
  Planarity :  0.004   0.056   1762
  Dihedral  :  3.913  17.874   1360
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.71 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.25), residues: 1248
  helix:  2.23 (0.17), residues: 876
  sheet: -0.17 (0.82), residues: 46
  loop : -1.83 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 624 
 HIS   0.003   0.000   HIS B 379 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.020   0.001   TYR B 368 
 ARG   0.007   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  697)
  hydrogen bonds       : angle       4.08859 ( 2067)
  covalent geometry    : bond        0.00297 (10440)
  covalent geometry    : angle       0.59425 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8045 (m-30) cc_final: 0.7683 (m-30)
REVERT: A    7 ILE cc_start: 0.9101 (mm) cc_final: 0.8849 (mm)
REVERT: A   30 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: A  448 MET cc_start: 0.7401 (ttm) cc_final: 0.6680 (tpt)
REVERT: A  511 MET cc_start: 0.7434 (mmm) cc_final: 0.6824 (mmm)
REVERT: A  521 MET cc_start: 0.8800 (tpp) cc_final: 0.8495 (tpp)
REVERT: A  677 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (mt-10)
REVERT: A  689 MET cc_start: 0.9173 (tpt) cc_final: 0.8931 (tpp)
REVERT: B   19 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7697 (m-80)
REVERT: B  387 PHE cc_start: 0.8438 (t80) cc_final: 0.8046 (t80)
REVERT: B  395 PHE cc_start: 0.8451 (t80) cc_final: 0.8196 (t80)
REVERT: B  521 MET cc_start: 0.9047 (tpp) cc_final: 0.8461 (tpp)
REVERT: B  525 TRP cc_start: 0.8733 (m-10) cc_final: 0.8376 (m-10)
REVERT: B  531 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: B  540 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8166 (tmm)
REVERT: B  677 GLU cc_start: 0.8084 (tt0) cc_final: 0.7832 (tt0)
  outliers start: 25
  outliers final: 16
  residues processed: 184
  average time/residue: 0.1643
  time to fit residues: 47.2912
Evaluate side-chains
  188 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 86 optimal weight:    0.0870
   chunk 85 optimal weight:   30.0000
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 92 optimal weight:    0.4980
   chunk 68 optimal weight:    0.5980
   chunk 115 optimal weight:    1.9990
   chunk 120 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
B 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.089935 restraints weight = 19915.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.092789 restraints weight = 10364.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.094609 restraints weight = 6988.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10440  Z= 0.114
  Angle     :  0.594  11.600  14200  Z= 0.286
  Chirality :  0.041   0.194   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.856  19.341   1360
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.27 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.25), residues: 1248
  helix:  2.23 (0.17), residues: 876
  sheet: -0.23 (0.81), residues: 46
  loop : -1.78 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B 379 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.013   0.001   TYR A 712 
 ARG   0.006   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03142 (  697)
  hydrogen bonds       : angle       4.07547 ( 2067)
  covalent geometry    : bond        0.00256 (10440)
  covalent geometry    : angle       0.59408 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8108 (m-30) cc_final: 0.7807 (m-30)
REVERT: A   30 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8637 (mm)
REVERT: A   93 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8381 (tt)
REVERT: A  448 MET cc_start: 0.7372 (ttm) cc_final: 0.6872 (tpt)
REVERT: A  521 MET cc_start: 0.8793 (tpp) cc_final: 0.8473 (tpp)
REVERT: A  534 MET cc_start: 0.8249 (mtt) cc_final: 0.7991 (mtt)
REVERT: A  677 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7819 (mt-10)
REVERT: A  689 MET cc_start: 0.9136 (tpt) cc_final: 0.8882 (tpp)
REVERT: B   19 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7704 (m-80)
REVERT: B  387 PHE cc_start: 0.8423 (t80) cc_final: 0.8046 (t80)
REVERT: B  395 PHE cc_start: 0.8381 (t80) cc_final: 0.8144 (t80)
REVERT: B  521 MET cc_start: 0.9068 (tpp) cc_final: 0.8567 (tpp)
REVERT: B  525 TRP cc_start: 0.8674 (m-10) cc_final: 0.8358 (m-10)
REVERT: B  531 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: B  540 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8225 (tmm)
REVERT: B  677 GLU cc_start: 0.8025 (tt0) cc_final: 0.7767 (tt0)
  outliers start: 23
  outliers final: 14
  residues processed: 180
  average time/residue: 0.1640
  time to fit residues: 46.3671
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  677 GLU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0970
   chunk 2 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.115474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.088231 restraints weight = 20106.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.091049 restraints weight = 10599.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092855 restraints weight = 7217.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10440  Z= 0.123
  Angle     :  0.615  11.449  14200  Z= 0.294
  Chirality :  0.041   0.200   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.847  18.642   1360
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.69 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.25), residues: 1248
  helix:  2.22 (0.17), residues: 876
  sheet: -0.33 (0.81), residues: 46
  loop : -1.76 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 624 
 HIS   0.002   0.000   HIS A 379 
 PHE   0.018   0.001   PHE B 471 
 TYR   0.023   0.001   TYR A 368 
 ARG   0.006   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  697)
  hydrogen bonds       : angle       4.06172 ( 2067)
  covalent geometry    : bond        0.00290 (10440)
  covalent geometry    : angle       0.61504 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8104 (m-30) cc_final: 0.7751 (m-30)
REVERT: A   30 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8688 (mm)
REVERT: A  534 MET cc_start: 0.8309 (mtt) cc_final: 0.8063 (mtt)
REVERT: A  689 MET cc_start: 0.9147 (tpt) cc_final: 0.8887 (tpp)
REVERT: B   19 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (m-80)
REVERT: B  164 VAL cc_start: 0.9162 (t) cc_final: 0.8920 (p)
REVERT: B  387 PHE cc_start: 0.8438 (t80) cc_final: 0.8061 (t80)
REVERT: B  395 PHE cc_start: 0.8371 (t80) cc_final: 0.8136 (t80)
REVERT: B  521 MET cc_start: 0.9077 (tpp) cc_final: 0.8111 (mmt)
REVERT: B  525 TRP cc_start: 0.8633 (m-10) cc_final: 0.7864 (m-10)
REVERT: B  531 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: B  677 GLU cc_start: 0.8103 (tt0) cc_final: 0.7861 (tt0)
  outliers start: 23
  outliers final: 16
  residues processed: 167
  average time/residue: 0.1655
  time to fit residues: 43.3536
Evaluate side-chains
  180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0060
   overall best weight:    0.7400

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.115189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.088229 restraints weight = 20026.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.090896 restraints weight = 10961.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.092590 restraints weight = 7598.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10440  Z= 0.125
  Angle     :  0.624  11.181  14200  Z= 0.298
  Chirality :  0.041   0.203   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.851  18.240   1360
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.69 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.25), residues: 1248
  helix:  2.23 (0.17), residues: 876
  sheet: -0.05 (0.83), residues: 44
  loop : -1.81 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 624 
 HIS   0.003   0.000   HIS B 379 
 PHE   0.018   0.001   PHE B 471 
 TYR   0.018   0.001   TYR B 469 
 ARG   0.006   0.000   ARG B 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  697)
  hydrogen bonds       : angle       4.05785 ( 2067)
  covalent geometry    : bond        0.00293 (10440)
  covalent geometry    : angle       0.62353 (14200)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A    6 ASP cc_start: 0.8072 (m-30) cc_final: 0.7771 (m-30)
REVERT: A   30 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8697 (mm)
REVERT: A  689 MET cc_start: 0.9154 (tpt) cc_final: 0.8903 (tpp)
REVERT: B   19 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7792 (m-80)
REVERT: B  387 PHE cc_start: 0.8434 (t80) cc_final: 0.8076 (t80)
REVERT: B  395 PHE cc_start: 0.8398 (t80) cc_final: 0.8144 (t80)
REVERT: B  521 MET cc_start: 0.9075 (tpp) cc_final: 0.8145 (mmt)
REVERT: B  531 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: B  677 GLU cc_start: 0.8052 (tt0) cc_final: 0.7831 (tt0)
  outliers start: 22
  outliers final: 16
  residues processed: 168
  average time/residue: 0.1770
  time to fit residues: 45.6461
Evaluate side-chains
  177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  455 THR
Chi-restraints excluded: chain B residue  641 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0970
   chunk 49 optimal weight:    0.2980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.115889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.088712 restraints weight = 19929.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.091485 restraints weight = 10638.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.093263 restraints weight = 7274.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10440  Z= 0.119
  Angle     :  0.624  11.094  14200  Z= 0.298
  Chirality :  0.041   0.204   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  3.833  18.388   1360
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.60 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.25), residues: 1248
  helix:  2.17 (0.17), residues: 888
  sheet: -0.11 (0.83), residues: 44
  loop : -1.78 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 624 
 HIS   0.002   0.000   HIS B 379 
 PHE   0.016   0.001   PHE B 471 
 TYR   0.028   0.001   TYR B 368 
 ARG   0.010   0.000   ARG A 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  697)
  hydrogen bonds       : angle       4.06464 ( 2067)
  covalent geometry    : bond        0.00276 (10440)
  covalent geometry    : angle       0.62353 (14200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3046.74 seconds
wall clock time: 53 minutes 43.06 seconds (3223.06 seconds total)