Starting phenix.real_space_refine
on Fri May 16 16:48:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r3k_18871/05_2025/8r3k_18871.cif"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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: 6
    Type Number    sf(0)   Gaussians
     P      45      5.49       5
     Mg      2      5.21       5
     S     104      5.16       5
     C    9143      2.51       5
     N    2567      2.21       5
     O    2906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14767
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 708, 5748
          Classifications: {'peptide': 708}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 675}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 708, 5748
          Classifications: {'peptide': 708}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 675}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 5858
    Chain: "B"
      Number of atoms: 5937
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 740, 5925
          Classifications: {'peptide': 740}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 740, 5925
          Classifications: {'peptide': 740}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6024
    Chain: "C"
      Number of atoms: 2024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2024
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
    Chain: "V"
      Number of atoms: 655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 655
          Classifications: {'RNA': 31}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 10, 'rna3p': 20}
    Chain: "M"
      Number of atoms: 222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 222
          Classifications: {'RNA': 10}
          Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 9}
    Chain: "G"
      Number of atoms: 159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 159
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 5, 'TRANS': 14}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 11
          Unusual residues: {' MG': 2, 'POP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 559 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 559 " occ=0.50
    residue:
      pdb=" N  ATYR B 557 " occ=0.70
      ... (22 atoms not shown)
      pdb=" OH BTYR B 557 " occ=0.30
  Time building chain proxies: 14.49, per 1000 atoms: 0.98
  Number of scatterers: 14767
  At special positions: 0
  Unit cell: (113.262, 98.336, 128.188, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     104     16.00
     P      45     15.00
     Mg      2     11.99
     O    2906      8.00
     N    2567      7.00
     C    9143      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: 3.86
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3254

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 16 sheets defined
      51.7% alpha, 13.0% beta
      12 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 4.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
    Processing helix  chain 'A' and resid 10 through 23
    Processing helix  chain 'A' and resid 31 through 50
      removed outlier: 3.820A  pdb=" N   PHE A  35 " --> pdb=" O   GLU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 126 through 139
      removed outlier: 3.727A  pdb=" N   TYR A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 3.707A  pdb=" N   ALA A 159 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 185
    Processing helix  chain 'A' and resid 187 through 194
    Processing helix  chain 'A' and resid 195 through 198
      removed outlier: 3.564A  pdb=" N   GLU A 198 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 195 through 198'
    Processing helix  chain 'A' and resid 209 through 217
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 240 through 249
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.577A  pdb=" N   TYR A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 382 through 384
      No H-bonds generated for 'chain 'A' and resid 382 through 384'
    Processing helix  chain 'A' and resid 405 through 415
      removed outlier: 3.555A  pdb=" N   SER A 409 " --> pdb=" O   CYS A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 451
    Processing helix  chain 'A' and resid 453 through 476
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.790A  pdb=" N   GLU A 538 " --> pdb=" O   HIS A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 580
    Processing helix  chain 'A' and resid 582 through 604
      removed outlier: 4.090A  pdb=" N   LEU A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLN A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 613
    Processing helix  chain 'A' and resid 632 through 650
    Processing helix  chain 'A' and resid 652 through 674
      removed outlier: 4.145A  pdb=" N   LYS A 664 " --> pdb=" O   ALA A 660 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A 665 " --> pdb=" O   GLU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 692
    Processing helix  chain 'A' and resid 697 through 716
      removed outlier: 4.091A  pdb=" N   ARG A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 17 through 22
      removed outlier: 3.576A  pdb=" N   PHE B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
    Processing helix  chain 'B' and resid 84 through 99
    Processing helix  chain 'B' and resid 101 through 116
    Processing helix  chain 'B' and resid 118 through 125
      removed outlier: 3.521A  pdb=" N   GLN B 124 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY B 125 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 161
      removed outlier: 3.535A  pdb=" N   GLU B 159 " --> pdb=" O   THR B 156 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER B 160 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 214 through 222
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 3.653A  pdb=" N   ARG B 249 " --> pdb=" O   GLY B 245 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   GLY B 250 " --> pdb=" O   MET B 246 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   PHE B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 265 " --> pdb=" O   SER B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 293
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.561A  pdb=" N   ASN B 312 " --> pdb=" O   TRP B 309 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN B 313 " --> pdb=" O   ASN B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 313'
    Processing helix  chain 'B' and resid 314 through 326
    Processing helix  chain 'B' and resid 330 through 345
      removed outlier: 4.660A  pdb=" N   ALA B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 369 through 376
      removed outlier: 4.014A  pdb=" N   ALA B 374 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE B 376 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 412 through 426
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 455 through 474
    Processing helix  chain 'B' and resid 504 through 509
      removed outlier: 3.641A  pdb=" N   MET B 507 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 540 through 560
    Processing helix  chain 'B' and resid 572 through 583
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 617 through 625
    Processing helix  chain 'B' and resid 679 through 700
      removed outlier: 4.355A  pdb=" N   ASP B 685 " --> pdb=" O   GLY B 681 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLU B 686 " --> pdb=" O   ILE B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 733
    Processing helix  chain 'B' and resid 736 through 756
    Processing helix  chain 'C' and resid 2 through 13
      removed outlier: 3.851A  pdb=" N   GLN C  13 " --> pdb=" O   ASP C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 23
    Processing helix  chain 'C' and resid 26 through 34
      removed outlier: 4.115A  pdb=" N   ILE C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 51
    Processing helix  chain 'C' and resid 62 through 66
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 3.616A  pdb=" N   VAL C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 115 through 128
    Processing helix  chain 'C' and resid 155 through 168
    Processing helix  chain 'C' and resid 169 through 172
      removed outlier: 3.729A  pdb=" N   VAL C 172 " --> pdb=" O   PRO C 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 169 through 172'
    Processing helix  chain 'C' and resid 179 through 193
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 231 through 236
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
      removed outlier: 3.629A  pdb=" N   LYS A  73 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.556A  pdb=" N   PHE A 117 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   HIS A 146 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLU A 119 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   PHE A 148 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   GLY A 121 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293
      removed outlier: 7.157A  pdb=" N   TYR A 501 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   LEU A 549 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N  AARG A 559 " --> pdb=" O   ASP A 547 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ASP A 547 " --> pdb=" O  AARG A 559 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   MET A 561 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL A 542 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293
      removed outlier: 6.588A  pdb=" N   MET A 485 " --> pdb=" O   TYR A 501 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   PHE A 503 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE A 483 " --> pdb=" O   PHE A 503 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE A 505 " --> pdb=" O   GLN A 481 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   GLN A 481 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   PHE A 480 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380
      removed outlier: 5.781A  pdb=" N   GLU A 377 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   GLN B 367 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL A 379 " --> pdb=" O   GLN B 367 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631
      removed outlier: 6.211A  pdb=" N   GLY A 631 " --> pdb=" O   PRO A 620 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181
    Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 192
      removed outlier: 3.570A  pdb=" N   ILE B 205 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244
      removed outlier: 3.575A  pdb=" N   THR B 226 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492
    Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668
      removed outlier: 4.477A  pdb=" N   ILE B 667 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   MET C  90 " --> pdb=" O   SER C  79 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135
      removed outlier: 5.161A  pdb=" N   MET C 243 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   GLU C 241 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148
      removed outlier: 6.586A  pdb=" N   LYS C 214 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)

    714 hydrogen bonds defined for protein.
    2002 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      29 hydrogen bonds
      58 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 5.35

  Time building geometry restraints manager: 4.44 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: 4621
        1.34 -     1.45: 2287
        1.45 -     1.57: 7974
        1.57 -     1.69: 91
        1.69 -     1.81: 179
  Bond restraints: 15152
  Sorted by residual:
  bond pdb=" CG  PRO A  28 "
       pdb=" CD  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.503  1.276  0.227 3.40e-02 8.65e+02 4.47e+01
  bond pdb=" N   PRO A  28 "
       pdb=" CD  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.473  1.519 -0.046 1.40e-02 5.10e+03 1.06e+01
  bond pdb=" CB  PRO A  28 "
       pdb=" CG  PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.654 -0.162 5.00e-02 4.00e+02 1.05e+01
  bond pdb=" O   POP B 801 "
       pdb=" P2  POP B 801 "
    ideal  model  delta    sigma   weight residual
    1.661  1.608  0.053 2.00e-02 2.50e+03 7.06e+00
  bond pdb=" O   POP B 801 "
       pdb=" P1  POP B 801 "
    ideal  model  delta    sigma   weight residual
    1.660  1.608  0.052 2.00e-02 2.50e+03 6.71e+00
  ... (remaining 15147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 20614
        3.84 -     7.68: 19
        7.68 -    11.51: 1
       11.51 -    15.35: 3
       15.35 -    19.19: 1
  Bond angle restraints: 20638
  Sorted by residual:
  angle pdb=" CA  PRO A  28 "
        pdb=" N   PRO A  28 "
        pdb=" CD  PRO A  28 "
      ideal   model   delta    sigma   weight residual
     112.00   97.83   14.17 1.40e+00 5.10e-01 1.02e+02
  angle pdb=" N   PRO A  28 "
        pdb=" CD  PRO A  28 "
        pdb=" CG  PRO A  28 "
      ideal   model   delta    sigma   weight residual
     103.20   89.31   13.89 1.50e+00 4.44e-01 8.58e+01
  angle pdb=" P1  POP B 801 "
        pdb=" O   POP B 801 "
        pdb=" P2  POP B 801 "
      ideal   model   delta    sigma   weight residual
     139.66  120.47   19.19 3.00e+00 1.11e-01 4.09e+01
  angle pdb=" CA  PRO A  28 "
        pdb=" CB  PRO A  28 "
        pdb=" CG  PRO A  28 "
      ideal   model   delta    sigma   weight residual
     104.50   95.32    9.18 1.90e+00 2.77e-01 2.34e+01
  angle pdb=" N   LEU B 753 "
        pdb=" CA  LEU B 753 "
        pdb=" C   LEU B 753 "
      ideal   model   delta    sigma   weight residual
     110.97  107.16    3.81 1.09e+00 8.42e-01 1.22e+01
  ... (remaining 20633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.46: 8798
       33.46 -    66.93: 491
       66.93 -   100.39: 31
      100.39 -   133.86: 1
      133.86 -   167.32: 2
  Dihedral angle restraints: 9323
    sinusoidal: 4298
      harmonic: 5025
  Sorted by residual:
  dihedral pdb=" O4'   U V  15 "
           pdb=" C1'   U V  15 "
           pdb=" N1    U V  15 "
           pdb=" C2    U V  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   45.92  154.08     1      1.50e+01 4.44e-03 8.10e+01
  dihedral pdb=" O4'   U V  31 "
           pdb=" C1'   U V  31 "
           pdb=" N1    U V  31 "
           pdb=" C2    U V  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   39.32 -167.32     1      1.70e+01 3.46e-03 6.56e+01
  dihedral pdb=" CA  ASP A 286 "
           pdb=" CB  ASP A 286 "
           pdb=" CG  ASP A 286 "
           pdb=" OD1 ASP A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.73   57.73     1      2.00e+01 2.50e-03 1.12e+01
  ... (remaining 9320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1677
       0.034 -    0.068: 443
       0.068 -    0.102: 107
       0.102 -    0.136: 48
       0.136 -    0.170: 6
  Chirality restraints: 2281
  Sorted by residual:
  chirality pdb=" CA  PRO A  28 "
            pdb=" N   PRO A  28 "
            pdb=" C   PRO A  28 "
            pdb=" CB  PRO A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  LEU B 753 "
            pdb=" N   LEU B 753 "
            pdb=" C   LEU B 753 "
            pdb=" CB  LEU B 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  ILE B 667 "
            pdb=" N   ILE B 667 "
            pdb=" C   ILE B 667 "
            pdb=" CB  ILE B 667 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 2278 not shown)

  Planarity restraints: 2502
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  27 "    0.049 5.00e-02 4.00e+02   6.75e-02 7.29e+00
        pdb=" N   PRO A  28 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 294 "   -0.036 5.00e-02 4.00e+02   5.41e-02 4.68e+00
        pdb=" N   PRO A 295 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 199 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO C 200 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C 200 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 200 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2499 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 102
        2.49 -     3.09: 10729
        3.09 -     3.70: 23021
        3.70 -     4.30: 34185
        4.30 -     4.90: 57402
  Nonbonded interactions: 125439
  Sorted by model distance:
  nonbonded pdb=" O2  POP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.888 2.170
  nonbonded pdb=" OD2 ASP B 305 "
            pdb="MG    MG B 803 "
     model   vdw
     2.004 2.170
  nonbonded pdb=" OD1 ASP B 445 "
            pdb="MG    MG B 803 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" OD2 ASP B 522 "
            pdb=" OH  TYR B 559 "
     model   vdw
     2.040 3.040
  nonbonded pdb=" OD1 ASP B 305 "
            pdb="MG    MG B 802 "
     model   vdw
     2.053 2.170
  ... (remaining 125434 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.050
  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:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     44.950
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
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      :  0.003   0.227  15152  Z= 0.142
  Angle     :  0.544  19.191  20638  Z= 0.288
  Chirality :  0.036   0.170   2281
  Planarity :  0.004   0.068   2502
  Dihedral  : 18.618 167.320   6069
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.85 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.23 (0.21), residues: 1703
  helix:  2.00 (0.19), residues: 827
  sheet: -0.06 (0.40), residues: 184
  loop : -0.36 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 706 
 HIS   0.003   0.001   HIS A 144 
 PHE   0.012   0.001   PHE B 740 
 TYR   0.011   0.001   TYR B 217 
 ARG   0.010   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12650 (  739)
  hydrogen bonds       : angle       5.33702 ( 2060)
  covalent geometry    : bond        0.00344 (15152)
  covalent geometry    : angle       0.54445 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.597 
Fit side-chains
REVERT: B  199 MET cc_start: 0.7630 (mmm) cc_final: 0.7372 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2850
  time to fit residues: 98.5623
Evaluate side-chains
  224 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 136 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 134 ASN
B 567 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.137026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109197 restraints weight = 34028.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.33
r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  15152  Z= 0.173
  Angle     :  0.565   7.128  20638  Z= 0.296
  Chirality :  0.041   0.165   2281
  Planarity :  0.004   0.043   2502
  Dihedral  : 13.004 171.203   2516
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 24.22 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.13 (0.20), residues: 1703
  helix:  1.92 (0.18), residues: 817
  sheet: -0.21 (0.38), residues: 186
  loop : -0.34 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 706 
 HIS   0.006   0.001   HIS A 713 
 PHE   0.015   0.001   PHE B 740 
 TYR   0.019   0.001   TYR A 130 
 ARG   0.007   0.001   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  739)
  hydrogen bonds       : angle       4.40224 ( 2060)
  covalent geometry    : bond        0.00411 (15152)
  covalent geometry    : angle       0.56512 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 227
  time to evaluate  : 1.492 
Fit side-chains
REVERT: A   52 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6424 (m90)
REVERT: A  361 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8534 (mmtp)
REVERT: A  524 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7925 (mt-10)
REVERT: B  407 MET cc_start: 0.8057 (tmm) cc_final: 0.7852 (tmm)
REVERT: B  449 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8416 (tt)
REVERT: B  567 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6364 (tm-30)
REVERT: B  608 GLU cc_start: 0.8378 (tt0) cc_final: 0.8110 (tt0)
REVERT: B  720 SER cc_start: 0.8931 (m) cc_final: 0.8676 (m)
REVERT: C  243 MET cc_start: 0.8569 (mmm) cc_final: 0.8363 (mmm)
  outliers start: 34
  outliers final: 16
  residues processed: 250
  average time/residue: 0.2852
  time to fit residues: 101.9041
Evaluate side-chains
  231 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  567 GLN
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  236 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 165 optimal weight:    1.9990
   chunk 148 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 597 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.134525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105107 restraints weight = 49264.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.98
r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  15152  Z= 0.163
  Angle     :  0.529   6.644  20638  Z= 0.277
  Chirality :  0.040   0.151   2281
  Planarity :  0.004   0.037   2502
  Dihedral  : 13.028 170.929   2516
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.63 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.20), residues: 1703
  helix:  1.85 (0.18), residues: 817
  sheet: -0.31 (0.37), residues: 186
  loop : -0.45 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 706 
 HIS   0.004   0.001   HIS A 510 
 PHE   0.013   0.001   PHE B 344 
 TYR   0.016   0.001   TYR B 217 
 ARG   0.009   0.001   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  739)
  hydrogen bonds       : angle       4.30226 ( 2060)
  covalent geometry    : bond        0.00387 (15152)
  covalent geometry    : angle       0.52942 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 222
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: A   52 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6437 (m90)
REVERT: A  130 TYR cc_start: 0.6832 (t80) cc_final: 0.6426 (t80)
REVERT: A  187 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.6051 (pp)
REVERT: A  202 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6886 (pt0)
REVERT: A  361 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8532 (mmtp)
REVERT: A  372 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8033 (tm-30)
REVERT: A  524 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7642 (mt-10)
REVERT: A  593 GLU cc_start: 0.8360 (tt0) cc_final: 0.7949 (tp30)
REVERT: A  625 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8450 (Cg_endo)
REVERT: B  407 MET cc_start: 0.7863 (tmm) cc_final: 0.7536 (tmm)
REVERT: B  449 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: B  720 SER cc_start: 0.8857 (m) cc_final: 0.8563 (m)
REVERT: C  187 LYS cc_start: 0.8267 (ptmt) cc_final: 0.7964 (ptmt)
REVERT: C  243 MET cc_start: 0.8516 (mmm) cc_final: 0.8291 (mmm)
  outliers start: 39
  outliers final: 25
  residues processed: 252
  average time/residue: 0.2983
  time to fit residues: 107.5690
Evaluate side-chains
  242 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 1.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   46 ARG
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  236 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 130 optimal weight:    0.0060
   chunk 109 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 172 optimal weight:    1.9990
   chunk 122 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0060
   chunk 57 optimal weight:    0.3980
   chunk 163 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 148 optimal weight:    0.0050
   overall best weight:    0.2026

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.139666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.110772 restraints weight = 42795.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.69
r_work: 0.3100 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  15152  Z= 0.101
  Angle     :  0.479   7.151  20638  Z= 0.250
  Chirality :  0.038   0.141   2281
  Planarity :  0.003   0.044   2502
  Dihedral  : 12.960 172.443   2516
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 23.50 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.20), residues: 1703
  helix:  1.97 (0.18), residues: 819
  sheet: -0.31 (0.37), residues: 185
  loop : -0.35 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  49 
 HIS   0.005   0.001   HIS A 510 
 PHE   0.011   0.001   PHE A  46 
 TYR   0.011   0.001   TYR B 559 
 ARG   0.009   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  739)
  hydrogen bonds       : angle       4.07013 ( 2060)
  covalent geometry    : bond        0.00224 (15152)
  covalent geometry    : angle       0.47861 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 232
  time to evaluate  : 1.574 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7798 (tm-30)
REVERT: A  130 TYR cc_start: 0.6760 (t80) cc_final: 0.6376 (t80)
REVERT: A  187 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5864 (pp)
REVERT: A  202 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6886 (pt0)
REVERT: A  372 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7957 (tm-30)
REVERT: A  388 ASN cc_start: 0.6867 (p0) cc_final: 0.6428 (p0)
REVERT: A  431 ASP cc_start: 0.7616 (m-30) cc_final: 0.7108 (p0)
REVERT: A  524 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7481 (mt-10)
REVERT: A  561 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8278 (tmm)
REVERT: A  593 GLU cc_start: 0.8221 (tt0) cc_final: 0.7820 (tp30)
REVERT: A  625 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8405 (Cg_endo)
REVERT: B  449 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8118 (tt)
REVERT: B  720 SER cc_start: 0.8829 (m) cc_final: 0.8540 (m)
REVERT: B  736 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7100 (pttt)
REVERT: C   11 MET cc_start: 0.8445 (mmm) cc_final: 0.8158 (tpt)
REVERT: C   46 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7536 (ttm170)
REVERT: C  187 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7954 (ptmt)
REVERT: C  243 MET cc_start: 0.8495 (mmm) cc_final: 0.8259 (mmm)
  outliers start: 38
  outliers final: 20
  residues processed: 257
  average time/residue: 0.3148
  time to fit residues: 116.6304
Evaluate side-chains
  240 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 1.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   46 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 153 optimal weight:    0.7980
   chunk 125 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 166 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.109183 restraints weight = 36649.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.45
r_work: 0.3090 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15152  Z= 0.140
  Angle     :  0.497   6.965  20638  Z= 0.259
  Chirality :  0.039   0.144   2281
  Planarity :  0.004   0.096   2502
  Dihedral  : 12.990 171.974   2516
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.50 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.04 (0.20), residues: 1703
  helix:  1.87 (0.18), residues: 819
  sheet: -0.16 (0.38), residues: 175
  loop : -0.46 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 706 
 HIS   0.020   0.001   HIS A 146 
 PHE   0.013   0.001   PHE A 148 
 TYR   0.017   0.001   TYR B 497 
 ARG   0.010   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  739)
  hydrogen bonds       : angle       4.09317 ( 2060)
  covalent geometry    : bond        0.00329 (15152)
  covalent geometry    : angle       0.49731 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 215
  time to evaluate  : 1.648 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: A   52 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6433 (m90)
REVERT: A  130 TYR cc_start: 0.6804 (t80) cc_final: 0.6448 (t80)
REVERT: A  187 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5892 (pp)
REVERT: A  192 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6943 (ttp-110)
REVERT: A  372 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8000 (tm-30)
REVERT: A  388 ASN cc_start: 0.6891 (p0) cc_final: 0.6507 (p0)
REVERT: A  431 ASP cc_start: 0.7661 (m-30) cc_final: 0.7203 (p0)
REVERT: A  524 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7554 (mt-10)
REVERT: A  561 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8331 (tmm)
REVERT: A  593 GLU cc_start: 0.8263 (tt0) cc_final: 0.7817 (tp30)
REVERT: A  629 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7094 (mt-10)
REVERT: B  449 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8218 (tt)
REVERT: B  567 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.6164 (tm-30)
REVERT: B  720 SER cc_start: 0.8815 (m) cc_final: 0.8509 (m)
REVERT: C   11 MET cc_start: 0.8457 (mmm) cc_final: 0.8119 (tpt)
REVERT: C  187 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7952 (ptmt)
  outliers start: 42
  outliers final: 27
  residues processed: 242
  average time/residue: 0.2826
  time to fit residues: 99.3000
Evaluate side-chains
  241 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 207
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  567 GLN
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0570
   chunk 111 optimal weight:    0.8980
   chunk 154 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0270
   chunk 64 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 132 optimal weight:    0.5980
   chunk 169 optimal weight:    4.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
B 671 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.108151 restraints weight = 51474.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.03
r_work: 0.3043 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15152  Z= 0.140
  Angle     :  0.504   7.548  20638  Z= 0.262
  Chirality :  0.039   0.186   2281
  Planarity :  0.004   0.037   2502
  Dihedral  : 12.984 171.994   2516
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.63 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.02 (0.20), residues: 1703
  helix:  1.86 (0.18), residues: 814
  sheet: -0.19 (0.38), residues: 175
  loop : -0.46 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 706 
 HIS   0.011   0.001   HIS A 146 
 PHE   0.012   0.001   PHE B 344 
 TYR   0.014   0.001   TYR B 497 
 ARG   0.008   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  739)
  hydrogen bonds       : angle       4.11646 ( 2060)
  covalent geometry    : bond        0.00328 (15152)
  covalent geometry    : angle       0.50406 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 218
  time to evaluate  : 1.644 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: A  130 TYR cc_start: 0.6761 (t80) cc_final: 0.6376 (t80)
REVERT: A  187 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5854 (pp)
REVERT: A  192 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6919 (ttp-110)
REVERT: A  372 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8046 (tm-30)
REVERT: A  431 ASP cc_start: 0.7738 (m-30) cc_final: 0.7271 (p0)
REVERT: A  524 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7651 (mt-10)
REVERT: A  561 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8393 (tmm)
REVERT: A  593 GLU cc_start: 0.8306 (tt0) cc_final: 0.7880 (tp30)
REVERT: A  629 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7249 (mt-10)
REVERT: B  449 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8258 (tt)
REVERT: B  720 SER cc_start: 0.8826 (m) cc_final: 0.8518 (m)
REVERT: C   38 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6646 (ttp-170)
REVERT: C  187 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7959 (ptmt)
  outliers start: 44
  outliers final: 33
  residues processed: 248
  average time/residue: 0.2902
  time to fit residues: 103.9038
Evaluate side-chains
  252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 213
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 163 optimal weight:    0.0870
   chunk 127 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 149 optimal weight:    2.9990
   chunk 152 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
B 671 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110782 restraints weight = 35331.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.33
r_work: 0.3110 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15152  Z= 0.110
  Angle     :  0.488   7.083  20638  Z= 0.254
  Chirality :  0.038   0.165   2281
  Planarity :  0.003   0.038   2502
  Dihedral  : 12.968 172.623   2516
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.63 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.20), residues: 1703
  helix:  1.95 (0.18), residues: 812
  sheet: -0.27 (0.37), residues: 185
  loop : -0.31 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 706 
 HIS   0.008   0.001   HIS A 146 
 PHE   0.011   0.001   PHE A  46 
 TYR   0.012   0.001   TYR B 497 
 ARG   0.009   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  739)
  hydrogen bonds       : angle       4.05908 ( 2060)
  covalent geometry    : bond        0.00252 (15152)
  covalent geometry    : angle       0.48791 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 218
  time to evaluate  : 1.651 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: A   52 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6470 (m90)
REVERT: A  187 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5914 (pp)
REVERT: A  202 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7160 (pt0)
REVERT: A  372 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8096 (tm-30)
REVERT: A  431 ASP cc_start: 0.7883 (m-30) cc_final: 0.7316 (p0)
REVERT: A  524 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7854 (mt-10)
REVERT: A  561 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8516 (tmm)
REVERT: A  593 GLU cc_start: 0.8401 (tt0) cc_final: 0.8008 (tp30)
REVERT: A  629 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7378 (mt-10)
REVERT: B  449 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8254 (tt)
REVERT: B  720 SER cc_start: 0.8822 (m) cc_final: 0.8520 (m)
REVERT: C   11 MET cc_start: 0.8554 (mmm) cc_final: 0.8245 (tpt)
REVERT: C  187 LYS cc_start: 0.8297 (ptmt) cc_final: 0.8027 (ptmt)
  outliers start: 43
  outliers final: 31
  residues processed: 247
  average time/residue: 0.2840
  time to fit residues: 102.9109
Evaluate side-chains
  253 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 215
  time to evaluate  : 1.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0970
   chunk 46 optimal weight:    0.6980
   chunk 172 optimal weight:    0.0170
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109939 restraints weight = 50154.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.97
r_work: 0.3075 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15152  Z= 0.111
  Angle     :  0.494   8.622  20638  Z= 0.257
  Chirality :  0.038   0.183   2281
  Planarity :  0.003   0.038   2502
  Dihedral  : 12.947 172.998   2516
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.50 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.10 (0.20), residues: 1703
  helix:  1.91 (0.18), residues: 818
  sheet: -0.08 (0.38), residues: 175
  loop : -0.42 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 706 
 HIS   0.007   0.001   HIS A 146 
 PHE   0.011   0.001   PHE B 699 
 TYR   0.011   0.001   TYR B 497 
 ARG   0.009   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03294 (  739)
  hydrogen bonds       : angle       4.03117 ( 2060)
  covalent geometry    : bond        0.00256 (15152)
  covalent geometry    : angle       0.49442 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 217
  time to evaluate  : 1.715 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: A   52 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6438 (m90)
REVERT: A  101 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7705 (mt-10)
REVERT: A  130 TYR cc_start: 0.6673 (t80) cc_final: 0.6409 (t80)
REVERT: A  187 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5869 (pp)
REVERT: A  192 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6877 (ttp-110)
REVERT: A  202 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6935 (pt0)
REVERT: A  372 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8000 (tm-30)
REVERT: A  431 ASP cc_start: 0.7696 (m-30) cc_final: 0.7263 (p0)
REVERT: A  524 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7520 (mt-10)
REVERT: A  561 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8365 (tmm)
REVERT: A  593 GLU cc_start: 0.8220 (tt0) cc_final: 0.7869 (tp30)
REVERT: A  629 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7218 (mt-10)
REVERT: B  449 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8168 (tt)
REVERT: B  718 MET cc_start: 0.8238 (mtm) cc_final: 0.7737 (mtm)
REVERT: B  720 SER cc_start: 0.8746 (m) cc_final: 0.8430 (m)
REVERT: C   11 MET cc_start: 0.8421 (mmm) cc_final: 0.8128 (tpt)
REVERT: C   38 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6331 (ttp-170)
REVERT: C  127 HIS cc_start: 0.6873 (m-70) cc_final: 0.6375 (m-70)
REVERT: C  187 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7972 (ptmt)
  outliers start: 45
  outliers final: 29
  residues processed: 247
  average time/residue: 0.2816
  time to fit residues: 101.8320
Evaluate side-chains
  253 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 215
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 82 optimal weight:    0.4980
   chunk 111 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 146 optimal weight:    4.9990
   chunk 153 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 314 ASN
B 425 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.109040 restraints weight = 41188.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.54
r_work: 0.3074 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15152  Z= 0.155
  Angle     :  0.524   8.100  20638  Z= 0.272
  Chirality :  0.040   0.214   2281
  Planarity :  0.004   0.035   2502
  Dihedral  : 12.967 172.894   2516
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.50 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.06 (0.20), residues: 1703
  helix:  1.85 (0.18), residues: 812
  sheet: -0.13 (0.38), residues: 175
  loop : -0.37 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 706 
 HIS   0.008   0.001   HIS A 146 
 PHE   0.015   0.001   PHE B 344 
 TYR   0.016   0.001   TYR B 217 
 ARG   0.009   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  739)
  hydrogen bonds       : angle       4.11437 ( 2060)
  covalent geometry    : bond        0.00364 (15152)
  covalent geometry    : angle       0.52355 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 215
  time to evaluate  : 1.676 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: A   52 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6499 (m90)
REVERT: A  101 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7661 (mt-10)
REVERT: A  130 TYR cc_start: 0.6731 (t80) cc_final: 0.6473 (t80)
REVERT: A  187 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5878 (pp)
REVERT: A  202 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6978 (pt0)
REVERT: A  372 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8014 (tm-30)
REVERT: A  431 ASP cc_start: 0.7718 (m-30) cc_final: 0.7303 (p0)
REVERT: A  524 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7523 (mt-10)
REVERT: A  551 ARG cc_start: 0.8360 (mmp-170) cc_final: 0.8080 (mmp-170)
REVERT: A  561 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8413 (tmm)
REVERT: A  593 GLU cc_start: 0.8286 (tt0) cc_final: 0.7866 (tp30)
REVERT: A  629 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7175 (mt-10)
REVERT: B  237 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8334 (mtmt)
REVERT: B  449 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8306 (tt)
REVERT: B  507 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8199 (mtm)
REVERT: B  716 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8128 (tm-30)
REVERT: B  720 SER cc_start: 0.8714 (m) cc_final: 0.8325 (m)
REVERT: C   38 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6292 (ttp-170)
REVERT: C  187 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7972 (ptmt)
  outliers start: 49
  outliers final: 34
  residues processed: 249
  average time/residue: 0.2965
  time to fit residues: 106.5153
Evaluate side-chains
  260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 214
  time to evaluate  : 1.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  142 LYS
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  237 LYS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  716 GLU
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 85 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 167 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 132 optimal weight:    0.0040
   chunk 135 optimal weight:    2.9990
   chunk 133 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 150 optimal weight:    0.2980
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.3592

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

Flipped N/Q/H residues before XYZ refinement:
B 314 ASN
B 425 ASN
B 671 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.137816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.109029 restraints weight = 43457.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.62
r_work: 0.3057 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.147  15152  Z= 0.194
  Angle     :  0.952  59.165  20638  Z= 0.580
  Chirality :  0.041   0.698   2281
  Planarity :  0.004   0.044   2502
  Dihedral  : 12.995 172.907   2516
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.83 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  1.08 (0.20), residues: 1703
  helix:  1.87 (0.18), residues: 812
  sheet: -0.13 (0.38), residues: 175
  loop : -0.37 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 706 
 HIS   0.007   0.001   HIS A 146 
 PHE   0.014   0.001   PHE B 344 
 TYR   0.015   0.001   TYR B 217 
 ARG   0.009   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  739)
  hydrogen bonds       : angle       4.13418 ( 2060)
  covalent geometry    : bond        0.00400 (15152)
  covalent geometry    : angle       0.95242 (20638)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 214
  time to evaluate  : 1.697 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: A   52 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6497 (m90)
REVERT: A  101 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (mt-10)
REVERT: A  130 TYR cc_start: 0.6727 (t80) cc_final: 0.6475 (t80)
REVERT: A  187 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5867 (pp)
REVERT: A  202 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6995 (pt0)
REVERT: A  372 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8024 (tm-30)
REVERT: A  431 ASP cc_start: 0.7713 (m-30) cc_final: 0.7302 (p0)
REVERT: A  524 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7532 (mt-10)
REVERT: A  551 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.8102 (mmp-170)
REVERT: A  561 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8423 (tmm)
REVERT: A  593 GLU cc_start: 0.8294 (tt0) cc_final: 0.7881 (tp30)
REVERT: A  629 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7189 (mt-10)
REVERT: B  237 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8348 (mtmt)
REVERT: B  449 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8305 (tt)
REVERT: B  716 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8165 (tm-30)
REVERT: B  720 SER cc_start: 0.8714 (m) cc_final: 0.8328 (m)
REVERT: C   38 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6506 (ttp-170)
REVERT: C  187 LYS cc_start: 0.8219 (ptmt) cc_final: 0.7977 (ptmt)
  outliers start: 46
  outliers final: 33
  residues processed: 247
  average time/residue: 0.2900
  time to fit residues: 103.3156
Evaluate side-chains
  256 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 212
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  142 LYS
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  258 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  402 SER
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  237 LYS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  709 VAL
Chi-restraints excluded: chain B residue  716 GLU
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  164 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 163 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 138 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 164 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0670
   chunk 129 optimal weight:    1.9990
   chunk 162 optimal weight:    0.9990
   chunk 166 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B 153 ASN
B 314 ASN
B 671 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.137221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.108095 restraints weight = 46084.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.72
r_work: 0.3071 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15152  Z= 0.135
  Angle     :  0.515   7.185  20638  Z= 0.269
  Chirality :  0.039   0.146   2281
  Planarity :  0.004   0.036   2502
  Dihedral  : 12.963 173.465   2516
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.96 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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:  1.09 (0.20), residues: 1703
  helix:  1.89 (0.18), residues: 812
  sheet: -0.22 (0.37), residues: 185
  loop : -0.34 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 706 
 HIS   0.006   0.001   HIS A 146 
 PHE   0.015   0.001   PHE B 344 
 TYR   0.013   0.001   TYR B 217 
 ARG   0.009   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  739)
  hydrogen bonds       : angle       4.08836 ( 2060)
  covalent geometry    : bond        0.00315 (15152)
  covalent geometry    : angle       0.51466 (20638)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7126.74 seconds
wall clock time: 124 minutes 27.87 seconds (7467.87 seconds total)