Starting phenix.real_space_refine
on Sat Oct 11 12:40:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r3k_18871/10_2025/8r3k_18871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r3k_18871/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r3k_18871/10_2025/8r3k_18871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r3k_18871/10_2025/8r3k_18871.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r3k_18871/10_2025/8r3k_18871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r3k_18871/10_2025/8r3k_18871.map"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.83, per 1000 atoms: 0.39
  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: 1.39
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 2.03
  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: 2.86

  Time building geometry restraints manager: 1.78 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:             4.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.360
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.650
-------------------------------------------------------------------------------
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 : 7.23
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.000   ARG A 124 
 TYR   0.011   0.001   TYR B 217 
 PHE   0.012   0.001   PHE B 740 
 TRP   0.019   0.001   TRP A 706 
 HIS   0.003   0.001   HIS A 144 

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

*********************** 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  : 0.574 
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: 0.1381
  time to fit residues: 47.9667
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  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.138021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.108860 restraints weight = 47347.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.82
r_work: 0.3049 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  15152  Z= 0.154
  Angle     :  0.543   6.929  20638  Z= 0.286
  Chirality :  0.040   0.154   2281
  Planarity :  0.004   0.044   2502
  Dihedral  : 12.993 171.593   2516
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 24.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.20), residues: 1703
  helix:  2.00 (0.18), residues: 816
  sheet: -0.16 (0.38), residues: 186
  loop : -0.33 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 124 
 TYR   0.018   0.001   TYR A 130 
 PHE   0.014   0.001   PHE B 740 
 TRP   0.018   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 713 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (15152)
  covalent geometry    : angle       0.54326 (20638)
  hydrogen bonds       : bond        0.04087 (  739)
  hydrogen bonds       : angle       4.35778 ( 2060)

*********************** 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
  255 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A   52 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6386 (m90)
REVERT: A  361 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8477 (mmtp)
REVERT: A  524 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7586 (mt-10)
REVERT: B  407 MET cc_start: 0.7831 (tmm) cc_final: 0.7616 (tmm)
REVERT: B  449 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8325 (tt)
REVERT: B  567 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6348 (tm-30)
REVERT: B  608 GLU cc_start: 0.8249 (tt0) cc_final: 0.8015 (tt0)
REVERT: B  720 SER cc_start: 0.8866 (m) cc_final: 0.8616 (m)
  outliers start: 29
  outliers final: 16
  residues processed: 247
  average time/residue: 0.1396
  time to fit residues: 49.6680
Evaluate side-chains
  229 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
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  304 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  444 ASN
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 142 optimal weight:    0.0020
   chunk 156 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 158 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.5790

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.136997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.108500 restraints weight = 52257.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.04
r_work: 0.3060 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    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 = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15152  Z= 0.132
  Angle     :  0.504   6.398  20638  Z= 0.264
  Chirality :  0.039   0.146   2281
  Planarity :  0.004   0.039   2502
  Dihedral  : 12.985 171.520   2516
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.11 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.20), residues: 1703
  helix:  1.93 (0.18), residues: 823
  sheet: -0.21 (0.38), residues: 186
  loop : -0.39 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 116 
 TYR   0.013   0.001   TYR B 217 
 PHE   0.011   0.001   PHE B 344 
 TRP   0.016   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (15152)
  covalent geometry    : angle       0.50420 (20638)
  hydrogen bonds       : bond        0.03725 (  739)
  hydrogen bonds       : angle       4.21884 ( 2060)

*********************** 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: 41
    poor density    : 220
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: A   52 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6398 (m90)
REVERT: A  130 TYR cc_start: 0.6814 (t80) cc_final: 0.6441 (t80)
REVERT: A  187 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5950 (pp)
REVERT: A  202 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6990 (pt0)
REVERT: A  361 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8563 (mmtp)
REVERT: A  372 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8012 (tm-30)
REVERT: A  388 ASN cc_start: 0.6810 (p0) cc_final: 0.6415 (p0)
REVERT: A  524 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7566 (mt-10)
REVERT: A  593 GLU cc_start: 0.8322 (tt0) cc_final: 0.7866 (tp30)
REVERT: B  449 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8241 (tt)
REVERT: B  720 SER cc_start: 0.8831 (m) cc_final: 0.8554 (m)
REVERT: B  736 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7124 (pttm)
REVERT: C   11 MET cc_start: 0.8520 (mmm) cc_final: 0.8253 (tpp)
REVERT: C   46 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7608 (ttm170)
REVERT: C  187 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7959 (ptmt)
  outliers start: 41
  outliers final: 22
  residues processed: 249
  average time/residue: 0.1425
  time to fit residues: 50.9597
Evaluate side-chains
  243 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  187 LEU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
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  130 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  321 MET
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  579 LEU
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 150 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 140 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109693 restraints weight = 35150.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.38
r_work: 0.3089 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15152  Z= 0.144
  Angle     :  0.505   6.961  20638  Z= 0.263
  Chirality :  0.039   0.145   2281
  Planarity :  0.004   0.089   2502
  Dihedral  : 13.026 171.439   2516
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.50 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.20), residues: 1703
  helix:  1.85 (0.18), residues: 821
  sheet: -0.18 (0.38), residues: 175
  loop : -0.48 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 287 
 TYR   0.014   0.001   TYR B 217 
 PHE   0.012   0.001   PHE A 148 
 TRP   0.019   0.001   TRP A 706 
 HIS   0.018   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15152)
  covalent geometry    : angle       0.50518 (20638)
  hydrogen bonds       : bond        0.03650 (  739)
  hydrogen bonds       : angle       4.16840 ( 2060)

*********************** 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
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 218
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: A   52 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6492 (m90)
REVERT: A  130 TYR cc_start: 0.6839 (t80) cc_final: 0.6463 (t80)
REVERT: A  166 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A  187 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5956 (pp)
REVERT: A  202 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7066 (pt0)
REVERT: A  361 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8620 (mmtp)
REVERT: A  372 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8099 (tm-30)
REVERT: A  388 ASN cc_start: 0.6928 (p0) cc_final: 0.6555 (p0)
REVERT: A  431 ASP cc_start: 0.7935 (m-30) cc_final: 0.7303 (p0)
REVERT: A  524 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7829 (mt-10)
REVERT: A  561 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8519 (tmm)
REVERT: A  593 GLU cc_start: 0.8499 (tt0) cc_final: 0.8034 (tp30)
REVERT: B  449 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: B  720 SER cc_start: 0.8914 (m) cc_final: 0.8626 (m)
REVERT: B  736 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7156 (pttt)
REVERT: C  187 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8018 (ptmt)
  outliers start: 39
  outliers final: 27
  residues processed: 243
  average time/residue: 0.1454
  time to fit residues: 50.9778
Evaluate side-chains
  243 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
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  155 MET
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  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  130 ASP
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  321 MET
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   36 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  236 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 173 optimal weight:    2.9990
   chunk 149 optimal weight:    0.0870
   chunk 108 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   chunk 161 optimal weight:    0.7980
   chunk 33 optimal weight:    0.2980
   chunk 110 optimal weight:    3.9990
   chunk 153 optimal weight:    0.9980
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
B 567 GLN
B 671 ASN
** B 687 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 = 0.3612 r_free = 0.3612 target = 0.139349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110994 restraints weight = 36525.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.46
r_work: 0.3109 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    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 = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  15152  Z= 0.105
  Angle     :  0.474   6.919  20638  Z= 0.249
  Chirality :  0.038   0.140   2281
  Planarity :  0.003   0.041   2502
  Dihedral  : 12.962 172.322   2516
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.20), residues: 1703
  helix:  2.03 (0.18), residues: 814
  sheet: -0.28 (0.37), residues: 185
  loop : -0.31 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 287 
 TYR   0.011   0.001   TYR B 555 
 PHE   0.010   0.001   PHE A  46 
 TRP   0.017   0.001   TRP A 706 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (15152)
  covalent geometry    : angle       0.47449 (20638)
  hydrogen bonds       : bond        0.03275 (  739)
  hydrogen bonds       : angle       4.04810 ( 2060)

*********************** 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
  268 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 227
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: A  130 TYR cc_start: 0.6752 (t80) cc_final: 0.6383 (t80)
REVERT: A  187 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5871 (pp)
REVERT: A  202 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6852 (pt0)
REVERT: A  372 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7985 (tm-30)
REVERT: A  388 ASN cc_start: 0.6872 (p0) cc_final: 0.6494 (p0)
REVERT: A  431 ASP cc_start: 0.7594 (m-30) cc_final: 0.7093 (p0)
REVERT: A  524 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7394 (mt-10)
REVERT: A  561 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8296 (tmm)
REVERT: A  593 GLU cc_start: 0.8226 (tt0) cc_final: 0.7781 (tp30)
REVERT: B  449 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: B  567 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6115 (tm-30)
REVERT: B  720 SER cc_start: 0.8811 (m) cc_final: 0.8509 (m)
REVERT: B  736 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7021 (pttt)
REVERT: C   11 MET cc_start: 0.8433 (mmm) cc_final: 0.8147 (tpt)
REVERT: C  187 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7955 (ptmt)
  outliers start: 41
  outliers final: 25
  residues processed: 258
  average time/residue: 0.1387
  time to fit residues: 51.9321
Evaluate side-chains
  245 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
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  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  130 ASP
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  302 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  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
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
Chi-restraints excluded: chain C residue  236 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 125 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 157 optimal weight:    0.8980
   chunk 127 optimal weight:    0.0870
   chunk 169 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B 671 ASN
** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110504 restraints weight = 31944.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.20
r_work: 0.3110 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1519

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= 0.132
  Angle     :  0.496   6.991  20638  Z= 0.258
  Chirality :  0.039   0.182   2281
  Planarity :  0.004   0.035   2502
  Dihedral  : 12.946 172.196   2516
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.76 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.20), residues: 1703
  helix:  1.90 (0.18), residues: 820
  sheet: -0.13 (0.38), residues: 175
  loop : -0.44 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 287 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.012   0.001   PHE A  46 
 TRP   0.023   0.001   TRP A 706 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (15152)
  covalent geometry    : angle       0.49558 (20638)
  hydrogen bonds       : bond        0.03393 (  739)
  hydrogen bonds       : angle       4.06862 ( 2060)

*********************** 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
  259 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 216
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: A   52 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6477 (m90)
REVERT: A  130 TYR cc_start: 0.6791 (t80) cc_final: 0.6411 (t80)
REVERT: A  187 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5898 (pp)
REVERT: A  192 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6803 (ttp-110)
REVERT: A  202 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7090 (pt0)
REVERT: A  372 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8102 (tm-30)
REVERT: A  388 ASN cc_start: 0.7075 (p0) cc_final: 0.6717 (p0)
REVERT: A  431 ASP cc_start: 0.7842 (m-30) cc_final: 0.7266 (p0)
REVERT: A  524 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (mt-10)
REVERT: A  561 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8471 (tmm)
REVERT: A  593 GLU cc_start: 0.8406 (tt0) cc_final: 0.7960 (tp30)
REVERT: A  629 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7321 (mt-10)
REVERT: B  449 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8237 (tt)
REVERT: B  720 SER cc_start: 0.8891 (m) cc_final: 0.8592 (m)
REVERT: B  736 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7055 (pttt)
REVERT: C   11 MET cc_start: 0.8579 (mmm) cc_final: 0.8240 (tpt)
REVERT: C   38 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6619 (ttp-170)
REVERT: C  171 GLU cc_start: 0.8244 (tp30) cc_final: 0.7948 (mp0)
  outliers start: 43
  outliers final: 31
  residues processed: 248
  average time/residue: 0.1371
  time to fit residues: 49.2608
Evaluate side-chains
  251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 212
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
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  109 LEU
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  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  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  130 ASP
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  302 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  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 132 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 160 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0770
   chunk 82 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
B 567 GLN
** B 687 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 = 0.3614 r_free = 0.3614 target = 0.139724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.111251 restraints weight = 41043.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.58
r_work: 0.3081 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15152  Z= 0.119
  Angle     :  0.491   7.004  20638  Z= 0.256
  Chirality :  0.038   0.145   2281
  Planarity :  0.003   0.037   2502
  Dihedral  : 12.927 172.658   2516
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.70 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.20), residues: 1703
  helix:  2.00 (0.18), residues: 808
  sheet: -0.21 (0.37), residues: 185
  loop : -0.29 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 287 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.011   0.001   PHE B 344 
 TRP   0.023   0.001   TRP A 706 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (15152)
  covalent geometry    : angle       0.49122 (20638)
  hydrogen bonds       : bond        0.03329 (  739)
  hydrogen bonds       : angle       4.06016 ( 2060)

*********************** 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
  260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 215
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A   21 MET cc_start: 0.8138 (ttp) cc_final: 0.7881 (ttt)
REVERT: A   52 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6438 (m90)
REVERT: A  130 TYR cc_start: 0.6766 (t80) cc_final: 0.6419 (t80)
REVERT: A  187 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5881 (pp)
REVERT: A  202 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6981 (pt0)
REVERT: A  372 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7997 (tm-30)
REVERT: A  431 ASP cc_start: 0.7673 (m-30) cc_final: 0.7211 (p0)
REVERT: A  524 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7459 (mt-10)
REVERT: A  561 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8332 (tmm)
REVERT: A  593 GLU cc_start: 0.8240 (tt0) cc_final: 0.7828 (tp30)
REVERT: A  629 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7172 (mt-10)
REVERT: B  449 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (tt)
REVERT: B  567 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6026 (tm-30)
REVERT: B  720 SER cc_start: 0.8828 (m) cc_final: 0.8534 (m)
REVERT: C   11 MET cc_start: 0.8448 (mmm) cc_final: 0.8104 (tpt)
REVERT: C   38 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6581 (ttp-170)
REVERT: C  127 HIS cc_start: 0.6931 (m-70) cc_final: 0.6435 (m-70)
REVERT: C  171 GLU cc_start: 0.8106 (tp30) cc_final: 0.7877 (mp0)
REVERT: C  187 LYS cc_start: 0.8245 (ptmt) cc_final: 0.8008 (ptmt)
REVERT: G   20 THR cc_start: 0.8568 (m) cc_final: 0.8306 (m)
  outliers start: 45
  outliers final: 31
  residues processed: 247
  average time/residue: 0.1415
  time to fit residues: 50.6936
Evaluate side-chains
  250 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  109 LEU
Chi-restraints excluded: chain A residue  162 THR
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  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  402 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  444 ASN
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  130 ASP
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  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  321 MET
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  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   38 ARG
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 147 optimal weight:    3.9990
   chunk 155 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 169 optimal weight:    4.9990
   chunk 139 optimal weight:    0.6980
   chunk 100 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 153 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.138481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110697 restraints weight = 31583.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.25
r_work: 0.3111 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1628

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= 0.126
  Angle     :  0.506   8.594  20638  Z= 0.262
  Chirality :  0.039   0.189   2281
  Planarity :  0.004   0.052   2502
  Dihedral  : 12.922 172.832   2516
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.20), residues: 1703
  helix:  1.96 (0.18), residues: 813
  sheet: -0.20 (0.36), residues: 185
  loop : -0.30 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 116 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.012   0.001   PHE B 344 
 TRP   0.027   0.001   TRP A 706 
 HIS   0.006   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (15152)
  covalent geometry    : angle       0.50649 (20638)
  hydrogen bonds       : bond        0.03346 (  739)
  hydrogen bonds       : angle       4.05602 ( 2060)

*********************** 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
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 213
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: A   21 MET cc_start: 0.8198 (ttp) cc_final: 0.7936 (ttt)
REVERT: A   52 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6468 (m90)
REVERT: A  187 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5897 (pp)
REVERT: A  202 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7107 (pt0)
REVERT: A  372 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8087 (tm-30)
REVERT: A  431 ASP cc_start: 0.7853 (m-30) cc_final: 0.7309 (p0)
REVERT: A  524 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7713 (mt-10)
REVERT: A  561 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8501 (tmm)
REVERT: A  593 GLU cc_start: 0.8388 (tt0) cc_final: 0.7965 (tp30)
REVERT: A  629 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7379 (mt-10)
REVERT: B  449 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8237 (tt)
REVERT: B  720 SER cc_start: 0.8885 (m) cc_final: 0.8597 (m)
REVERT: B  736 LYS cc_start: 0.7541 (mmpt) cc_final: 0.6742 (pttt)
REVERT: C   11 MET cc_start: 0.8608 (mmm) cc_final: 0.8258 (tpt)
REVERT: C   38 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6533 (ttp-170)
REVERT: C  127 HIS cc_start: 0.7121 (m-70) cc_final: 0.6624 (m-70)
REVERT: C  171 GLU cc_start: 0.8221 (tp30) cc_final: 0.7898 (mp0)
REVERT: C  187 LYS cc_start: 0.8316 (ptmt) cc_final: 0.8040 (ptmt)
REVERT: G   20 THR cc_start: 0.8570 (m) cc_final: 0.8326 (m)
  outliers start: 44
  outliers final: 32
  residues processed: 244
  average time/residue: 0.1391
  time to fit residues: 49.4224
Evaluate side-chains
  249 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 209
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
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  109 LEU
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  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  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  130 ASP
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  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  321 MET
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  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   38 ARG
Chi-restraints excluded: chain C residue   50 MET
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 38 optimal weight:    3.9990
   chunk 136 optimal weight:    0.2980
   chunk 67 optimal weight:    0.5980
   chunk 116 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 108 optimal weight:    0.0670
   chunk 127 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
B 425 ASN
B 567 GLN
** 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 = 0.3613 r_free = 0.3613 target = 0.139645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110799 restraints weight = 57087.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 3.25
r_work: 0.2909 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1691

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= 0.121
  Angle     :  0.504   7.567  20638  Z= 0.262
  Chirality :  0.039   0.188   2281
  Planarity :  0.003   0.036   2502
  Dihedral  : 12.911 173.400   2516
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 23.89 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.20), residues: 1703
  helix:  1.96 (0.18), residues: 813
  sheet: -0.18 (0.36), residues: 185
  loop : -0.30 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 287 
 TYR   0.013   0.001   TYR A 130 
 PHE   0.012   0.001   PHE B 344 
 TRP   0.029   0.001   TRP A 706 
 HIS   0.006   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (15152)
  covalent geometry    : angle       0.50419 (20638)
  hydrogen bonds       : bond        0.03353 (  739)
  hydrogen bonds       : angle       4.04778 ( 2060)

*********************** 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
  261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 214
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: A   21 MET cc_start: 0.8250 (ttp) cc_final: 0.7992 (ttt)
REVERT: A  130 TYR cc_start: 0.6630 (t80) cc_final: 0.6312 (t80)
REVERT: A  187 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5844 (pp)
REVERT: A  202 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7030 (pt0)
REVERT: A  372 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8112 (tm-30)
REVERT: A  431 ASP cc_start: 0.7719 (m-30) cc_final: 0.7230 (p0)
REVERT: A  524 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7553 (mt-10)
REVERT: A  551 ARG cc_start: 0.8407 (mmp-170) cc_final: 0.8153 (tpm170)
REVERT: A  561 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8427 (tmm)
REVERT: A  593 GLU cc_start: 0.8275 (tt0) cc_final: 0.7859 (tp30)
REVERT: A  629 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7275 (mt-10)
REVERT: B  449 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8168 (tt)
REVERT: B  507 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8251 (mtm)
REVERT: B  567 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6048 (tm-30)
REVERT: B  720 SER cc_start: 0.8872 (m) cc_final: 0.8600 (m)
REVERT: B  736 LYS cc_start: 0.7675 (mmpt) cc_final: 0.6817 (pttt)
REVERT: C   11 MET cc_start: 0.8511 (mmm) cc_final: 0.8187 (tpt)
REVERT: C   38 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6207 (ttp-170)
REVERT: C  127 HIS cc_start: 0.7026 (m-70) cc_final: 0.6530 (m-70)
REVERT: C  171 GLU cc_start: 0.8173 (tp30) cc_final: 0.7878 (mp0)
REVERT: C  187 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7990 (ptmt)
REVERT: G   20 THR cc_start: 0.8563 (m) cc_final: 0.8303 (m)
  outliers start: 47
  outliers final: 35
  residues processed: 248
  average time/residue: 0.1447
  time to fit residues: 52.1153
Evaluate side-chains
  253 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 209
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  162 THR
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  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  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  130 ASP
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  302 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  425 ASN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  507 MET
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   38 ARG
Chi-restraints excluded: chain C residue   50 MET
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 70 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    0.4980
   chunk 78 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 160 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0770
   chunk 86 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 ASN
B 567 GLN
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 = 0.3610 r_free = 0.3610 target = 0.139509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.110777 restraints weight = 43183.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.63
r_work: 0.3087 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111  15152  Z= 0.194
  Angle     :  0.923  59.172  20638  Z= 0.549
  Chirality :  0.043   0.698   2281
  Planarity :  0.004   0.041   2502
  Dihedral  : 12.936 173.406   2516
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.20), residues: 1703
  helix:  1.97 (0.18), residues: 813
  sheet: -0.20 (0.36), residues: 190
  loop : -0.29 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 287 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.012   0.001   PHE B 344 
 TRP   0.028   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (15152)
  covalent geometry    : angle       0.92256 (20638)
  hydrogen bonds       : bond        0.03421 (  739)
  hydrogen bonds       : angle       4.06515 ( 2060)

********************** 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
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7785 (tm-30)
REVERT: A   21 MET cc_start: 0.8220 (ttp) cc_final: 0.7973 (ttt)
REVERT: A  130 TYR cc_start: 0.6643 (t80) cc_final: 0.6340 (t80)
REVERT: A  187 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5833 (pp)
REVERT: A  202 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6961 (pt0)
REVERT: A  372 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: A  431 ASP cc_start: 0.7666 (m-30) cc_final: 0.7226 (p0)
REVERT: A  524 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7455 (mt-10)
REVERT: A  551 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.8158 (tpm170)
REVERT: A  561 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8375 (tmm)
REVERT: A  593 GLU cc_start: 0.8225 (tt0) cc_final: 0.7830 (tp30)
REVERT: A  629 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7177 (mt-10)
REVERT: B  449 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8172 (tt)
REVERT: B  716 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8158 (tm-30)
REVERT: B  720 SER cc_start: 0.8831 (m) cc_final: 0.8460 (m)
REVERT: B  736 LYS cc_start: 0.7668 (mmpt) cc_final: 0.6829 (pttt)
REVERT: C   11 MET cc_start: 0.8445 (mmm) cc_final: 0.8137 (tpt)
REVERT: C   38 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6258 (ttp-170)
REVERT: C  127 HIS cc_start: 0.6927 (m-70) cc_final: 0.6438 (m-70)
REVERT: C  171 GLU cc_start: 0.8116 (tp30) cc_final: 0.7883 (mp0)
REVERT: C  187 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7985 (ptmt)
REVERT: G   20 THR cc_start: 0.8582 (m) cc_final: 0.8324 (m)
  outliers start: 46
  outliers final: 37
  residues processed: 244
  average time/residue: 0.1264
  time to fit residues: 45.1484
Evaluate side-chains
  252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 207
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  162 THR
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  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  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  130 ASP
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  302 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  321 MET
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  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  716 GLU
Chi-restraints excluded: chain B residue  728 ILE
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   76 THR
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 119 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 116 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 112 optimal weight:   50.0000
   chunk 132 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0470
   chunk 11 optimal weight:    7.9990
   chunk 104 optimal weight:    0.6980
   chunk 150 optimal weight:    0.0270
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 ASN
B 567 GLN
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 = 0.3590 r_free = 0.3590 target = 0.137653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.108418 restraints weight = 43771.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.71
r_work: 0.3081 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.295  15152  Z= 0.221
  Angle     :  0.904  57.131  20638  Z= 0.593
  Chirality :  0.042   0.697   2281
  Planarity :  0.004   0.097   2502
  Dihedral  : 12.936 173.406   2516
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.76 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.20), residues: 1703
  helix:  1.97 (0.18), residues: 813
  sheet: -0.20 (0.36), residues: 190
  loop : -0.29 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 287 
 TYR   0.012   0.001   TYR B 217 
 PHE   0.012   0.001   PHE B 344 
 TRP   0.028   0.001   TRP A 706 
 HIS   0.005   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (15152)
  covalent geometry    : angle       0.90389 (20638)
  hydrogen bonds       : bond        0.03421 (  739)
  hydrogen bonds       : angle       4.06510 ( 2060)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3620.48 seconds
wall clock time: 63 minutes 0.66 seconds (3780.66 seconds total)