Starting phenix.real_space_refine
on Fri Jun 13 16:20:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fff_50355/06_2025/9fff_50355.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      63      5.49       5
     S      67      5.16       5
     C    9329      2.51       5
     N    2726      2.21       5
     O    2860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15045
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1119, 7054
          Classifications: {'peptide': 1119}
          Incomplete info: {'backbone_only': 326, 'truncation_to_alanine': 147}
          Link IDs: {'PTRANS': 46, 'TRANS': 1072}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 1877
          Unresolved non-hydrogen angles: 2600
          Unresolved non-hydrogen dihedrals: 1243
          Unresolved non-hydrogen chiralities: 453
          Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 25, 'TRP:plan': 2, 'ASP:plan': 48, 'PHE:plan': 18, 'GLU:plan': 58, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 980
    Chain: "B"
      Number of atoms: 6661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 950, 6661
          Classifications: {'peptide': 950}
          Incomplete info: {'backbone_only': 107, 'truncation_to_alanine': 136}
          Link IDs: {'PTRANS': 27, 'TRANS': 922}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 873
          Unresolved non-hydrogen angles: 1161
          Unresolved non-hydrogen dihedrals: 600
          Unresolved non-hydrogen chiralities: 156
          Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 33, 'PHE:plan': 2, 'GLU:plan': 34, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 495
    Chain: "S"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 657
          Classifications: {'DNA': 32}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 31}
    Chain: "T"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 673
          Classifications: {'DNA': 33}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 32}
  Time building chain proxies: 10.61, per 1000 atoms: 0.71
  Number of scatterers: 15045
  At special positions: 0
  Unit cell: (101.475, 165.825, 137.775, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      67     16.00
     P      63     15.00
     O    2860      8.00
     N    2726      7.00
     C    9329      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.94
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3108

  Finding SS restraints...
    Secondary structure from input PDB file:
      112 helices and 2 sheets defined
      78.5% alpha, 0.5% beta
      21 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 6.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 75 through 88
    Processing helix  chain 'A' and resid 91 through 108
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 3.633A  pdb=" N   LEU A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 145
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 3.944A  pdb=" N   ALA A 151 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 207 through 217
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 226 through 240
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 244 through 255
      removed outlier: 4.094A  pdb=" N   ILE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 273
      removed outlier: 4.014A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LYS A 264 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 292
      removed outlier: 3.516A  pdb=" N   VAL A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 296
      No H-bonds generated for 'chain 'A' and resid 294 through 296'
    Processing helix  chain 'A' and resid 297 through 309
    Processing helix  chain 'A' and resid 351 through 360
      removed outlier: 3.820A  pdb=" N   GLN A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 376
      removed outlier: 3.944A  pdb=" N   TRP A 367 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
    Processing helix  chain 'A' and resid 402 through 412
      removed outlier: 3.664A  pdb=" N   LEU A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 427
    Processing helix  chain 'A' and resid 428 through 434
      removed outlier: 3.846A  pdb=" N   PHE A 434 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.370A  pdb=" N   LEU A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLN A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   THR A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   HIS A 447 " --> pdb=" O   GLN A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 466
    Processing helix  chain 'A' and resid 469 through 486
    Processing helix  chain 'A' and resid 488 through 506
      removed outlier: 3.602A  pdb=" N   ASP A 501 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 524
      removed outlier: 4.282A  pdb=" N   TYR A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   THR A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   PHE A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 540
      removed outlier: 4.222A  pdb=" N   ILE A 538 " --> pdb=" O   LYS A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 550 through 566
      removed outlier: 3.564A  pdb=" N   GLN A 554 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   SER A 566 " --> pdb=" O   ARG A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 588
      removed outlier: 4.212A  pdb=" N   ILE A 577 " --> pdb=" O   LYS A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.547A  pdb=" N   LEU A 612 " --> pdb=" O   CYS A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 645
      removed outlier: 4.494A  pdb=" N   LEU A 630 " --> pdb=" O   THR A 626 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ALA A 631 " --> pdb=" O   PRO A 627 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LYS A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 659 through 668
      Proline residue:  A 665  - end of helix
    Processing helix  chain 'A' and resid 702 through 708
    Processing helix  chain 'A' and resid 728 through 733
      removed outlier: 4.137A  pdb=" N   SER A 733 " --> pdb=" O   PRO A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 735 through 747
      removed outlier: 3.519A  pdb=" N   GLU A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 771
    Processing helix  chain 'A' and resid 772 through 777
      removed outlier: 3.789A  pdb=" N   SER A 777 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 802
      removed outlier: 3.617A  pdb=" N   ASN A 793 " --> pdb=" O   PHE A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 835
      removed outlier: 4.035A  pdb=" N   LYS A 830 " --> pdb=" O   ASN A 826 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   CYS A 831 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 924
    Processing helix  chain 'A' and resid 928 through 935
      removed outlier: 4.029A  pdb=" N   VAL A 931 " --> pdb=" O   ASP A 928 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   SER A 933 " --> pdb=" O   GLU A 930 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   VAL A 934 " --> pdb=" O   VAL A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 979
      removed outlier: 3.663A  pdb=" N   TRP A 973 " --> pdb=" O   ASP A 969 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LYS A 974 " --> pdb=" O   ASP A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1005
    Processing helix  chain 'A' and resid 1007 through 1017
    Processing helix  chain 'A' and resid 1018 through 1036
      removed outlier: 3.800A  pdb=" N   LEU A1022 " --> pdb=" O   LEU A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1072
      removed outlier: 4.224A  pdb=" N   LEU A1055 " --> pdb=" O   GLN A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1078
    Processing helix  chain 'A' and resid 1081 through 1097
      removed outlier: 3.877A  pdb=" N   VAL A1091 " --> pdb=" O   SER A1087 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LEU A1092 " --> pdb=" O   ALA A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1119
    Processing helix  chain 'A' and resid 1120 through 1122
      No H-bonds generated for 'chain 'A' and resid 1120 through 1122'
    Processing helix  chain 'A' and resid 1126 through 1141
    Processing helix  chain 'A' and resid 1146 through 1163
    Processing helix  chain 'A' and resid 1176 through 1193
      removed outlier: 3.569A  pdb=" N   SER A1180 " --> pdb=" O   SER A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1214
      removed outlier: 4.770A  pdb=" N   VAL A1208 " --> pdb=" O   SER A1204 " (cutoff:3.500A)
      Proline residue:  A1209  - end of helix
    Processing helix  chain 'A' and resid 1230 through 1248
      removed outlier: 3.703A  pdb=" N   PHE A1234 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1264
    Processing helix  chain 'A' and resid 1265 through 1285
      removed outlier: 3.649A  pdb=" N   LYS A1283 " --> pdb=" O   ILE A1279 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL A1284 " --> pdb=" O   ASN A1280 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE A1285 " --> pdb=" O   LEU A1281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1287 through 1317
      removed outlier: 4.577A  pdb=" N   MET A1310 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
      Proline residue:  A1311  - end of helix
      removed outlier: 4.567A  pdb=" N   HIS A1315 " --> pdb=" O   PRO A1311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1348
      removed outlier: 4.389A  pdb=" N   GLN A1337 " --> pdb=" O   LEU A1333 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A1338 " --> pdb=" O   SER A1334 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   HIS A1339 " --> pdb=" O   THR A1335 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   HIS A1340 " --> pdb=" O   ARG A1336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1350 through 1355
    Processing helix  chain 'A' and resid 1356 through 1378
      removed outlier: 3.581A  pdb=" N   LEU A1360 " --> pdb=" O   HIS A1356 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS A1372 " --> pdb=" O   VAL A1368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 224
    Processing helix  chain 'B' and resid 228 through 246
      removed outlier: 4.175A  pdb=" N   GLU B 246 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 284
    Processing helix  chain 'B' and resid 285 through 287
      No H-bonds generated for 'chain 'B' and resid 285 through 287'
    Processing helix  chain 'B' and resid 288 through 302
      removed outlier: 3.998A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B 293 " --> pdb=" O   GLU B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 321
      removed outlier: 3.589A  pdb=" N   LYS B 321 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 348
      removed outlier: 3.505A  pdb=" N   ILE B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 356
      removed outlier: 3.825A  pdb=" N   GLN B 353 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
      removed outlier: 3.717A  pdb=" N   VAL B 365 " --> pdb=" O   ASP B 361 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL B 370 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LYS B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 396
      removed outlier: 3.603A  pdb=" N   GLU B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 435
    Processing helix  chain 'B' and resid 438 through 451
    Processing helix  chain 'B' and resid 458 through 472
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 3.592A  pdb=" N   PHE B 487 " --> pdb=" O   THR B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 512
      Proline residue:  B 507  - end of helix
    Processing helix  chain 'B' and resid 512 through 528
      removed outlier: 3.502A  pdb=" N   GLN B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LYS B 525 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 549
      removed outlier: 3.962A  pdb=" N   ALA B 538 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG B 547 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 595
      removed outlier: 4.923A  pdb=" N   GLY B 591 " --> pdb=" O   LEU B 587 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   SER B 592 " --> pdb=" O   GLU B 588 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LEU B 593 " --> pdb=" O   ILE B 589 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ARG B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 616
      removed outlier: 4.112A  pdb=" N   MET B 606 " --> pdb=" O   ASP B 602 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU B 607 " --> pdb=" O   VAL B 603 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR B 608 " --> pdb=" O   ARG B 604 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   TYR B 612 " --> pdb=" O   TYR B 608 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   ASP B 613 " --> pdb=" O   GLU B 609 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   VAL B 614 " --> pdb=" O   GLY B 610 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ARG B 616 " --> pdb=" O   TYR B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 638
      removed outlier: 3.840A  pdb=" N   TYR B 636 " --> pdb=" O   GLN B 632 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   LEU B 638 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 653
    Processing helix  chain 'B' and resid 666 through 684
    Processing helix  chain 'B' and resid 701 through 718
    Processing helix  chain 'B' and resid 736 through 764
      removed outlier: 3.520A  pdb=" N   GLY B 751 " --> pdb=" O   ILE B 747 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL B 755 " --> pdb=" O   GLY B 751 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 767 through 785
      removed outlier: 3.513A  pdb=" N   CYS B 780 " --> pdb=" O   GLY B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 821
    Processing helix  chain 'B' and resid 830 through 838
    Processing helix  chain 'B' and resid 838 through 859
      removed outlier: 3.593A  pdb=" N   VAL B 846 " --> pdb=" O   MET B 842 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 848 " --> pdb=" O   TYR B 844 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ALA B 849 " --> pdb=" O   ALA B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 869 through 891
      removed outlier: 3.683A  pdb=" N   THR B 881 " --> pdb=" O   LEU B 877 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ARG B 882 " --> pdb=" O   CYS B 878 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL B 883 " --> pdb=" O   LYS B 879 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 884 " --> pdb=" O   ILE B 880 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE B 891 " --> pdb=" O   ARG B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 906 through 925
      removed outlier: 3.741A  pdb=" N   CYS B 910 " --> pdb=" O   ILE B 906 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU B 912 " --> pdb=" O   LEU B 908 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN B 919 " --> pdb=" O   LEU B 915 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLN B 923 " --> pdb=" O   ASN B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 937
      removed outlier: 3.985A  pdb=" N   ASP B 937 " --> pdb=" O   LEU B 933 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 949 through 971
      removed outlier: 3.604A  pdb=" N   LYS B 953 " --> pdb=" O   ASN B 949 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER B 964 " --> pdb=" O   GLN B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 977 through 992
      removed outlier: 3.775A  pdb=" N   LEU B 988 " --> pdb=" O   LEU B 984 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 999 through 1016
      removed outlier: 3.705A  pdb=" N   LEU B1003 " --> pdb=" O   SER B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1020 through 1035
      removed outlier: 3.527A  pdb=" N   PHE B1032 " --> pdb=" O   LEU B1028 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1041 through 1056
    Processing helix  chain 'B' and resid 1075 through 1079
    Processing helix  chain 'B' and resid 1080 through 1085
      removed outlier: 3.808A  pdb=" N   CYS B1084 " --> pdb=" O   ALA B1080 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1085 through 1106
      removed outlier: 3.809A  pdb=" N   TRP B1100 " --> pdb=" O   GLU B1096 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B1101 " --> pdb=" O   GLU B1097 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1122 through 1146
    Processing helix  chain 'B' and resid 1152 through 1177
      removed outlier: 3.897A  pdb=" N   ASP B1156 " --> pdb=" O   GLY B1152 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA B1167 " --> pdb=" O   SER B1163 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B1171 " --> pdb=" O   ALA B1167 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE B1173 " --> pdb=" O   LEU B1169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1188 through 1202
    Processing helix  chain 'B' and resid 1202 through 1222
      removed outlier: 3.763A  pdb=" N   ASN B1215 " --> pdb=" O   THR B1211 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER B1222 " --> pdb=" O   SER B1218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1242 through 1250
    Processing helix  chain 'B' and resid 1251 through 1275
      removed outlier: 4.240A  pdb=" N   ASN B1255 " --> pdb=" O   LYS B1251 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR B1263 " --> pdb=" O   ALA B1259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1294 through 1298
    Processing sheet with id=AA1, first strand: chain 'A' and resid 685 through 687
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1385 through 1388
      removed outlier: 3.665A  pdb=" N   TRP A1385 " --> pdb=" O   ARG B1291 " (cutoff:3.500A)

    1061 hydrogen bonds defined for protein.
    3123 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 6.81

  Time building geometry restraints manager: 4.48 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: 4716
        1.34 -     1.46: 2422
        1.46 -     1.58: 8082
        1.58 -     1.70: 126
        1.70 -     1.82: 95
  Bond restraints: 15441
  Sorted by residual:
  bond pdb=" CA  VAL A 273 "
       pdb=" CB  VAL A 273 "
    ideal  model  delta    sigma   weight residual
    1.539  1.524  0.015 5.40e-03 3.43e+04 8.17e+00
  bond pdb=" N   LYS A 400 "
       pdb=" CA  LYS A 400 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.84e+00
  bond pdb=" C   VAL A1357 "
       pdb=" N   PRO A1358 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.30e-02 5.92e+03 6.37e+00
  bond pdb=" N   SER A 393 "
       pdb=" CA  SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.32e-02 5.74e+03 6.02e+00
  bond pdb=" N   HIS A 392 "
       pdb=" CA  HIS A 392 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.20e-02 6.94e+03 3.46e+00
  ... (remaining 15436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 20827
        2.42 -     4.84: 216
        4.84 -     7.26: 43
        7.26 -     9.69: 8
        9.69 -    12.11: 3
  Bond angle restraints: 21097
  Sorted by residual:
  angle pdb=" CA  MET A 270 "
        pdb=" CB  MET A 270 "
        pdb=" CG  MET A 270 "
      ideal   model   delta    sigma   weight residual
     114.10  122.61   -8.51 2.00e+00 2.50e-01 1.81e+01
  angle pdb=" C   ILE A 391 "
        pdb=" N   HIS A 392 "
        pdb=" CA  HIS A 392 "
      ideal   model   delta    sigma   weight residual
     120.54  115.16    5.38 1.35e+00 5.49e-01 1.59e+01
  angle pdb=" N   MET A 270 "
        pdb=" CA  MET A 270 "
        pdb=" CB  MET A 270 "
      ideal   model   delta    sigma   weight residual
     110.28  115.80   -5.52 1.55e+00 4.16e-01 1.27e+01
  angle pdb=" CA  LEU A 792 "
        pdb=" CB  LEU A 792 "
        pdb=" CG  LEU A 792 "
      ideal   model   delta    sigma   weight residual
     116.30  128.41  -12.11 3.50e+00 8.16e-02 1.20e+01
  angle pdb=" CB  MET B 392 "
        pdb=" CG  MET B 392 "
        pdb=" SD  MET B 392 "
      ideal   model   delta    sigma   weight residual
     112.70  122.88  -10.18 3.00e+00 1.11e-01 1.15e+01
  ... (remaining 21092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.99: 7797
       32.99 -    65.99: 594
       65.99 -    98.98: 45
       98.98 -   131.98: 1
      131.98 -   164.97: 1
  Dihedral angle restraints: 8438
    sinusoidal: 3245
      harmonic: 5193
  Sorted by residual:
  dihedral pdb=" C4'  DC T  44 "
           pdb=" C3'  DC T  44 "
           pdb=" O3'  DC T  44 "
           pdb=" P    DT T  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   55.03  164.97     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" CA  GLU B 790 "
           pdb=" C   GLU B 790 "
           pdb=" N   LYS B 791 "
           pdb=" CA  LYS B 791 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.32   17.68     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ARG A1172 "
           pdb=" C   ARG A1172 "
           pdb=" N   GLU A1173 "
           pdb=" CA  GLU A1173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.93  -17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 8435 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 2215
       0.082 -    0.165: 100
       0.165 -    0.247: 2
       0.247 -    0.329: 1
       0.329 -    0.411: 1
  Chirality restraints: 2319
  Sorted by residual:
  chirality pdb=" CG  LEU A1064 "
            pdb=" CB  LEU A1064 "
            pdb=" CD1 LEU A1064 "
            pdb=" CD2 LEU A1064 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CG  LEU B 590 "
            pdb=" CB  LEU B 590 "
            pdb=" CD1 LEU B 590 "
            pdb=" CD2 LEU B 590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CB  ILE A1132 "
            pdb=" CA  ILE A1132 "
            pdb=" CG1 ILE A1132 "
            pdb=" CG2 ILE A1132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 2316 not shown)

  Planarity restraints: 2556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 586 "   -0.015 2.00e-02 2.50e+03   2.97e-02 8.83e+00
        pdb=" C   CYS B 586 "    0.051 2.00e-02 2.50e+03
        pdb=" O   CYS B 586 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU B 587 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B1080 "   -0.041 5.00e-02 4.00e+02   6.30e-02 6.34e+00
        pdb=" N   PRO B1081 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B1081 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B1081 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 528 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO A 529 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 529 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 529 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2553 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 323
        2.68 -     3.24: 16064
        3.24 -     3.79: 24936
        3.79 -     4.35: 30413
        4.35 -     4.90: 46718
  Nonbonded interactions: 118454
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 688 "
            pdb=" OG1 THR A 816 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" O   ALA B1167 "
            pdb=" OG1 THR B1170 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OD1 ASN B1075 "
            pdb=" OG1 THR B1078 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   LEU A 927 "
            pdb=" NZ  LYS A 974 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" O   THR B1136 "
            pdb=" OG1 THR B1139 "
     model   vdw
     2.213 3.040
  ... (remaining 118449 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     43.230
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
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   0.045  15441  Z= 0.138
  Angle     :  0.646  12.107  21097  Z= 0.328
  Chirality :  0.039   0.411   2319
  Planarity :  0.004   0.063   2556
  Dihedral  : 20.681 164.971   5330
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.44 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 33.05 %
    Favored  : 66.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.20), residues: 2025
  helix:  1.53 (0.14), residues: 1402
  sheet:  None (None), residues: 0
  loop : -1.46 (0.27), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1165 
 HIS   0.005   0.001   HIS A1061 
 PHE   0.028   0.001   PHE A1235 
 TYR   0.014   0.001   TYR A1297 
 ARG   0.005   0.000   ARG A1336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19203 ( 1113)
  hydrogen bonds       : angle       6.20326 ( 3211)
  covalent geometry    : bond        0.00282 (15441)
  covalent geometry    : angle       0.64634 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 1.485 
Fit side-chains
REVERT: A  394 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6720 (m)
REVERT: A 1243 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: B  462 ILE cc_start: 0.9164 (pt) cc_final: 0.8878 (mm)
REVERT: B  873 MET cc_start: 0.8129 (mmm) cc_final: 0.7609 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2098
  time to fit residues: 35.8614
Evaluate side-chains
  97 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  400 LYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 179 optimal weight:    0.7980
   chunk 160 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0470
   chunk 108 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 166 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 192 optimal weight:    2.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
A1119 ASN
A1280 ASN
A1332 GLN
B 531 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.081813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.064643 restraints weight = 102858.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.065825 restraints weight = 60004.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.066107 restraints weight = 42326.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15441  Z= 0.150
  Angle     :  0.619   8.821  21097  Z= 0.321
  Chirality :  0.040   0.251   2319
  Planarity :  0.004   0.061   2556
  Dihedral  : 19.572 164.338   2864
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.84 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.78 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.19), residues: 2025
  helix:  1.47 (0.14), residues: 1465
  sheet:  None (None), residues: 0
  loop : -1.76 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1008 
 HIS   0.004   0.001   HIS B1175 
 PHE   0.031   0.001   PHE A1067 
 TYR   0.016   0.001   TYR A1297 
 ARG   0.003   0.000   ARG A1336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05207 ( 1113)
  hydrogen bonds       : angle       4.38475 ( 3211)
  covalent geometry    : bond        0.00319 (15441)
  covalent geometry    : angle       0.61890 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 100
  time to evaluate  : 1.537 
Fit side-chains
REVERT: A  732 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.3985 (mm)
REVERT: A  736 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6051 (t80)
REVERT: A 1243 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7895 (tm-30)
REVERT: B 1154 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.5735 (t)
  outliers start: 50
  outliers final: 22
  residues processed: 145
  average time/residue: 0.1973
  time to fit residues: 48.0610
Evaluate side-chains
  119 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  736 PHE
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1069 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  921 MET
Chi-restraints excluded: chain B residue 1074 VAL
Chi-restraints excluded: chain B residue 1088 LEU
Chi-restraints excluded: chain B residue 1136 THR
Chi-restraints excluded: chain B residue 1142 HIS
Chi-restraints excluded: chain B residue 1154 CYS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 128 optimal weight:   30.0000
   chunk 77 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 168 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0870
   chunk 58 optimal weight:    1.9990
   chunk 120 optimal weight:   10.0000
   chunk 78 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 157 optimal weight:    5.9990
   overall best weight:    1.1962

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.081928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.064787 restraints weight = 101951.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.066400 restraints weight = 60458.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.066373 restraints weight = 38323.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15441  Z= 0.139
  Angle     :  0.599   8.549  21097  Z= 0.306
  Chirality :  0.039   0.227   2319
  Planarity :  0.004   0.059   2556
  Dihedral  : 19.543 163.610   2857
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.54 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 31.12 %
    Favored  : 64.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.20), residues: 2025
  helix:  1.55 (0.14), residues: 1476
  sheet:  None (None), residues: 0
  loop : -1.71 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1268 
 HIS   0.003   0.001   HIS B1269 
 PHE   0.018   0.001   PHE A1131 
 TYR   0.019   0.001   TYR A1297 
 ARG   0.004   0.000   ARG A1336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04665 ( 1113)
  hydrogen bonds       : angle       4.13095 ( 3211)
  covalent geometry    : bond        0.00304 (15441)
  covalent geometry    : angle       0.59909 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 99
  time to evaluate  : 1.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  732 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.4030 (mm)
REVERT: A  736 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6013 (t80)
REVERT: B  462 ILE cc_start: 0.9131 (pt) cc_final: 0.8898 (mm)
REVERT: B  873 MET cc_start: 0.8079 (mmm) cc_final: 0.7761 (mmm)
REVERT: B 1086 LEU cc_start: 0.7731 (pp) cc_final: 0.7445 (tt)
REVERT: B 1154 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.5720 (t)
  outliers start: 57
  outliers final: 31
  residues processed: 147
  average time/residue: 0.1941
  time to fit residues: 48.4239
Evaluate side-chains
  128 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  736 PHE
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1069 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  921 MET
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1067 SER
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1142 HIS
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1154 CYS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 137 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 209 optimal weight:   20.0000
   chunk 197 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0370
   chunk 9 optimal weight:   50.0000
   chunk 207 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   overall best weight:    4.6064

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

Flipped N/Q/H residues before XYZ refinement:
A1034 GLN
A1325 GLN
A1339 HIS
A1379 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.079024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.062151 restraints weight = 104752.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.062671 restraints weight = 66860.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.062910 restraints weight = 44133.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  15441  Z= 0.310
  Angle     :  0.775  11.049  21097  Z= 0.404
  Chirality :  0.045   0.190   2319
  Planarity :  0.005   0.051   2556
  Dihedral  : 19.797 163.177   2857
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  8.07 %
    Allowed  : 28.68 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.19), residues: 2025
  helix:  0.96 (0.14), residues: 1470
  sheet:  None (None), residues: 0
  loop : -1.79 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1148 
 HIS   0.006   0.001   HIS A1030 
 PHE   0.038   0.003   PHE B 961 
 TYR   0.024   0.002   TYR A1297 
 ARG   0.006   0.001   ARG A1336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05609 ( 1113)
  hydrogen bonds       : angle       4.83396 ( 3211)
  covalent geometry    : bond        0.00661 (15441)
  covalent geometry    : angle       0.77457 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 87
  time to evaluate  : 1.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  732 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4570 (mm)
REVERT: A 1060 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7246 (t80)
REVERT: B  705 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9110 (m-10)
REVERT: B  716 MET cc_start: 0.9170 (mmp) cc_final: 0.8701 (mmm)
REVERT: B  817 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8251 (mm)
  outliers start: 96
  outliers final: 68
  residues processed: 173
  average time/residue: 0.1990
  time to fit residues: 57.7956
Evaluate side-chains
  155 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 83
  time to evaluate  : 1.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  664 PHE
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue  972 CYS
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1033 PHE
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1150 ARG
Chi-restraints excluded: chain A residue 1156 LEU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1260 VAL
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1340 HIS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  817 LEU
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  857 GLU
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  982 GLN
Chi-restraints excluded: chain B residue 1030 LEU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1067 SER
Chi-restraints excluded: chain B residue 1074 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1078 THR
Chi-restraints excluded: chain B residue 1088 LEU
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1138 LEU
Chi-restraints excluded: chain B residue 1142 HIS
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1171 SER
Chi-restraints excluded: chain B residue 1173 ILE
Chi-restraints excluded: chain B residue 1175 HIS
Chi-restraints excluded: chain B residue 1206 CYS
Chi-restraints excluded: chain B residue 1209 PHE
Chi-restraints excluded: chain B residue 1260 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 158 optimal weight:    0.0030
   chunk 71 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 155 optimal weight:    0.0570
   chunk 108 optimal weight:    0.5980
   chunk 12 optimal weight:   20.0000
   chunk 90 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.7312

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

Flipped N/Q/H residues before XYZ refinement:
B1201 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.082172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.065079 restraints weight = 105254.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.066205 restraints weight = 63788.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.066788 restraints weight = 40744.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  15441  Z= 0.131
  Angle     :  0.625   9.364  21097  Z= 0.313
  Chirality :  0.039   0.202   2319
  Planarity :  0.004   0.058   2556
  Dihedral  : 19.670 159.682   2855
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 32.88 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.20), residues: 2025
  helix:  1.37 (0.14), residues: 1478
  sheet:  None (None), residues: 0
  loop : -1.75 (0.29), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1148 
 HIS   0.004   0.001   HIS A1340 
 PHE   0.019   0.002   PHE B 961 
 TYR   0.018   0.001   TYR A1297 
 ARG   0.003   0.000   ARG A 737 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04503 ( 1113)
  hydrogen bonds       : angle       4.15784 ( 3211)
  covalent geometry    : bond        0.00286 (15441)
  covalent geometry    : angle       0.62482 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 97
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
REVERT: A 1060 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: B  462 ILE cc_start: 0.9107 (pt) cc_final: 0.8858 (mm)
REVERT: B  705 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.9083 (m-10)
REVERT: B  716 MET cc_start: 0.9243 (mmp) cc_final: 0.8778 (mmm)
REVERT: B  873 MET cc_start: 0.8125 (mmm) cc_final: 0.7770 (mmm)
REVERT: B 1086 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7438 (tt)
REVERT: B 1279 MET cc_start: 0.6799 (mmt) cc_final: 0.6596 (mmt)
  outliers start: 53
  outliers final: 36
  residues processed: 142
  average time/residue: 0.1977
  time to fit residues: 46.7507
Evaluate side-chains
  130 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1342 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1086 LEU
Chi-restraints excluded: chain B residue 1130 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1175 HIS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:    0.2980
   chunk 187 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 200 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 206 optimal weight:   10.0000
   chunk 140 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.081317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.063861 restraints weight = 103968.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.065489 restraints weight = 60950.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.065607 restraints weight = 37668.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15441  Z= 0.149
  Angle     :  0.624  10.608  21097  Z= 0.315
  Chirality :  0.040   0.175   2319
  Planarity :  0.004   0.056   2556
  Dihedral  : 19.640 159.321   2855
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.68 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 32.30 %
    Favored  : 62.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.20), residues: 2025
  helix:  1.42 (0.14), residues: 1485
  sheet:  None (None), residues: 0
  loop : -1.76 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1148 
 HIS   0.003   0.001   HIS B1175 
 PHE   0.025   0.001   PHE A1131 
 TYR   0.026   0.002   TYR A 634 
 ARG   0.004   0.000   ARG A1150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04546 ( 1113)
  hydrogen bonds       : angle       4.13845 ( 3211)
  covalent geometry    : bond        0.00329 (15441)
  covalent geometry    : angle       0.62443 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 91
  time to evaluate  : 1.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6091 (t80)
REVERT: A 1060 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6893 (t80)
REVERT: B  462 ILE cc_start: 0.9127 (pt) cc_final: 0.8882 (mm)
REVERT: B  705 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.9101 (m-10)
REVERT: B  716 MET cc_start: 0.9208 (mmp) cc_final: 0.8743 (mmm)
REVERT: B  873 MET cc_start: 0.8221 (mmm) cc_final: 0.7866 (mmm)
REVERT: B 1086 LEU cc_start: 0.7750 (pp) cc_final: 0.7338 (tt)
REVERT: B 1279 MET cc_start: 0.7087 (mmt) cc_final: 0.6811 (mmt)
  outliers start: 59
  outliers final: 41
  residues processed: 143
  average time/residue: 0.1982
  time to fit residues: 48.5938
Evaluate side-chains
  132 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 88
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  664 PHE
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  736 PHE
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1060 TYR
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1342 CYS
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1074 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1170 THR
Chi-restraints excluded: chain B residue 1175 HIS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 145 optimal weight:    5.9990
   chunk 110 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 177 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    1.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.080890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.063343 restraints weight = 104044.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.065152 restraints weight = 61544.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.065149 restraints weight = 35703.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15441  Z= 0.165
  Angle     :  0.646  14.098  21097  Z= 0.326
  Chirality :  0.040   0.204   2319
  Planarity :  0.004   0.056   2556
  Dihedral  : 19.624 158.268   2855
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.58 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 31.29 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.20), residues: 2025
  helix:  1.39 (0.14), residues: 1485
  sheet:  None (None), residues: 0
  loop : -1.83 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1148 
 HIS   0.007   0.001   HIS B1142 
 PHE   0.019   0.002   PHE A1131 
 TYR   0.021   0.002   TYR A 634 
 ARG   0.003   0.000   ARG A1150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 ( 1113)
  hydrogen bonds       : angle       4.21596 ( 3211)
  covalent geometry    : bond        0.00364 (15441)
  covalent geometry    : angle       0.64578 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 90
  time to evaluate  : 1.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  732 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4177 (mm)
REVERT: B  462 ILE cc_start: 0.9128 (pt) cc_final: 0.8886 (mm)
REVERT: B  705 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.9101 (m-10)
REVERT: B  716 MET cc_start: 0.9206 (mmp) cc_final: 0.8743 (mmm)
REVERT: B  873 MET cc_start: 0.8189 (mmm) cc_final: 0.7860 (mmm)
REVERT: B 1279 MET cc_start: 0.7322 (mmt) cc_final: 0.6876 (mmt)
  outliers start: 72
  outliers final: 54
  residues processed: 151
  average time/residue: 0.2028
  time to fit residues: 51.4848
Evaluate side-chains
  144 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 88
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  664 PHE
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1033 PHE
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1282 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue 1030 LEU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1074 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1138 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1175 HIS
Chi-restraints excluded: chain B residue 1206 CYS
Chi-restraints excluded: chain B residue 1213 VAL
Chi-restraints excluded: chain B residue 1260 ILE
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 199 optimal weight:    0.4980
   chunk 139 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 170 optimal weight:    0.7980
   chunk 5 optimal weight:   50.0000
   chunk 159 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.082037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.064342 restraints weight = 102469.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.065662 restraints weight = 58615.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.066531 restraints weight = 39820.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15441  Z= 0.125
  Angle     :  0.624  11.306  21097  Z= 0.307
  Chirality :  0.039   0.245   2319
  Planarity :  0.004   0.059   2556
  Dihedral  : 19.495 156.102   2855
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.74 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 32.30 %
    Favored  : 62.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.20), residues: 2025
  helix:  1.56 (0.14), residues: 1484
  sheet:  None (None), residues: 0
  loop : -1.73 (0.29), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1268 
 HIS   0.010   0.001   HIS B1142 
 PHE   0.016   0.001   PHE A1131 
 TYR   0.020   0.001   TYR A 634 
 ARG   0.004   0.000   ARG B1160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 ( 1113)
  hydrogen bonds       : angle       3.97081 ( 3211)
  covalent geometry    : bond        0.00273 (15441)
  covalent geometry    : angle       0.62436 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 96
  time to evaluate  : 1.627 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8549 (mm)
REVERT: A  732 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.3936 (mm)
REVERT: B  462 ILE cc_start: 0.9099 (pt) cc_final: 0.8817 (mm)
REVERT: B  705 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9107 (m-10)
REVERT: B  716 MET cc_start: 0.9213 (mmp) cc_final: 0.8734 (mmm)
REVERT: B  873 MET cc_start: 0.8215 (mmm) cc_final: 0.7912 (mmm)
REVERT: B 1086 LEU cc_start: 0.7712 (pp) cc_final: 0.7340 (tp)
REVERT: B 1279 MET cc_start: 0.7329 (mmt) cc_final: 0.6997 (mmt)
  outliers start: 56
  outliers final: 38
  residues processed: 145
  average time/residue: 0.2035
  time to fit residues: 49.2765
Evaluate side-chains
  131 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 90
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  857 GLU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1206 CYS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 57 optimal weight:    0.0170
   chunk 5 optimal weight:   50.0000
   chunk 199 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 188 optimal weight:    4.9990
   chunk 172 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    2.1824

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.080554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.062762 restraints weight = 102491.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.064037 restraints weight = 57687.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.064908 restraints weight = 38837.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15441  Z= 0.178
  Angle     :  0.668  11.968  21097  Z= 0.335
  Chirality :  0.042   0.236   2319
  Planarity :  0.004   0.056   2556
  Dihedral  : 19.517 155.664   2855
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.63 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 32.04 %
    Favored  : 63.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.20), residues: 2025
  helix:  1.43 (0.14), residues: 1488
  sheet:  None (None), residues: 0
  loop : -1.79 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A1268 
 HIS   0.007   0.001   HIS B1142 
 PHE   0.028   0.002   PHE A1131 
 TYR   0.020   0.002   TYR A 634 
 ARG   0.003   0.000   ARG A1068 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 ( 1113)
  hydrogen bonds       : angle       4.18637 ( 3211)
  covalent geometry    : bond        0.00392 (15441)
  covalent geometry    : angle       0.66836 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 92
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8559 (mm)
REVERT: A  732 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4037 (mm)
REVERT: B  314 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8871 (mp)
REVERT: B  462 ILE cc_start: 0.9137 (pt) cc_final: 0.8867 (mm)
REVERT: B  705 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.9082 (m-10)
REVERT: B  716 MET cc_start: 0.9170 (mmp) cc_final: 0.8705 (mmm)
REVERT: B  873 MET cc_start: 0.8270 (mmm) cc_final: 0.7973 (mmm)
REVERT: B 1086 LEU cc_start: 0.7728 (pp) cc_final: 0.7291 (tt)
REVERT: B 1279 MET cc_start: 0.7421 (mmt) cc_final: 0.6886 (mmt)
  outliers start: 57
  outliers final: 46
  residues processed: 143
  average time/residue: 0.1976
  time to fit residues: 47.8186
Evaluate side-chains
  139 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 89
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  664 PHE
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  789 PHE
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1245 SER
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  857 GLU
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue 1030 LEU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1138 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1175 HIS
Chi-restraints excluded: chain B residue 1206 CYS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 163 optimal weight:    0.9980
   chunk 120 optimal weight:    6.9990
   chunk 197 optimal weight:    5.9990
   chunk 132 optimal weight:    0.6980
   chunk 151 optimal weight:   10.0000
   chunk 107 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 181 optimal weight:    3.9990
   chunk 173 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4138 r_free = 0.4138 target = 0.082023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.064217 restraints weight = 104250.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.065564 restraints weight = 58730.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.066454 restraints weight = 39548.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15441  Z= 0.125
  Angle     :  0.645  14.499  21097  Z= 0.316
  Chirality :  0.040   0.267   2319
  Planarity :  0.004   0.059   2556
  Dihedral  : 19.447 153.477   2855
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.40 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 33.22 %
    Favored  : 62.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.20), residues: 2025
  helix:  1.55 (0.14), residues: 1483
  sheet:  None (None), residues: 0
  loop : -1.77 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1268 
 HIS   0.010   0.001   HIS B1142 
 PHE   0.038   0.001   PHE A1131 
 TYR   0.019   0.001   TYR A 634 
 ARG   0.004   0.000   ARG B1160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04410 ( 1113)
  hydrogen bonds       : angle       4.00296 ( 3211)
  covalent geometry    : bond        0.00273 (15441)
  covalent geometry    : angle       0.64523 (21097)

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

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

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4050 Ramachandran restraints generated.
    2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 97
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8515 (mm)
REVERT: A  732 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3727 (mm)
REVERT: B  314 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8921 (mp)
REVERT: B  462 ILE cc_start: 0.9102 (pt) cc_final: 0.8837 (mm)
REVERT: B  705 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.9068 (m-10)
REVERT: B  716 MET cc_start: 0.9142 (mmp) cc_final: 0.8667 (mmm)
REVERT: B  873 MET cc_start: 0.8116 (mmm) cc_final: 0.7841 (mmm)
REVERT: B 1086 LEU cc_start: 0.7573 (pp) cc_final: 0.7134 (tp)
REVERT: B 1279 MET cc_start: 0.7317 (mmt) cc_final: 0.6913 (mmt)
  outliers start: 47
  outliers final: 40
  residues processed: 138
  average time/residue: 0.1968
  time to fit residues: 46.0036
Evaluate side-chains
  135 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 91
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  923 TYR
Chi-restraints excluded: chain A residue 1061 HIS
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1148 TRP
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1249 ILE
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  614 VAL
Chi-restraints excluded: chain B residue  668 HIS
Chi-restraints excluded: chain B residue  705 PHE
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  853 VAL
Chi-restraints excluded: chain B residue  857 GLU
Chi-restraints excluded: chain B residue 1030 LEU
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1061 GLN
Chi-restraints excluded: chain B residue 1063 VAL
Chi-restraints excluded: chain B residue 1098 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1149 LEU
Chi-restraints excluded: chain B residue 1168 ILE
Chi-restraints excluded: chain B residue 1206 CYS
Chi-restraints excluded: chain B residue 1281 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 203 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 110 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0770
   chunk 188 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 208 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 111 optimal weight:    0.5980
   chunk 132 optimal weight:    0.9990
   chunk 162 optimal weight:    0.7980
   overall best weight:    1.0942

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.081731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.064791 restraints weight = 104430.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.066074 restraints weight = 62516.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.066472 restraints weight = 38904.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15441  Z= 0.133
  Angle     :  0.646  13.228  21097  Z= 0.316
  Chirality :  0.040   0.271   2319
  Planarity :  0.004   0.058   2556
  Dihedral  : 19.402 152.455   2855
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.94 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 33.39 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.20), residues: 2025
  helix:  1.58 (0.14), residues: 1485
  sheet:  None (None), residues: 0
  loop : -1.75 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1268 
 HIS   0.009   0.001   HIS B1142 
 PHE   0.030   0.001   PHE A1131 
 TYR   0.020   0.001   TYR A 634 
 ARG   0.005   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 ( 1113)
  hydrogen bonds       : angle       3.99983 ( 3211)
  covalent geometry    : bond        0.00293 (15441)
  covalent geometry    : angle       0.64556 (21097)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5486.01 seconds
wall clock time: 95 minutes 40.98 seconds (5740.98 seconds total)