Starting phenix.real_space_refine
on Thu Sep 18 17:08:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mr1_23953/09_2025/7mr1_23953.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      87      5.16       5
     C   11667      2.51       5
     N    3264      2.21       5
     O    3455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18473
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 6852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 858, 6852
          Classifications: {'peptide': 858}
          Link IDs: {'PTRANS': 34, 'TRANS': 823}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 8915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1101, 8915
          Classifications: {'peptide': 1101}
          Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1035}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2706
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 16, 'TRANS': 340}
  Time building chain proxies: 4.50, per 1000 atoms: 0.24
  Number of scatterers: 18473
  At special positions: 0
  Unit cell: (141.25, 126.56, 166.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      87     16.00
     O    3455      8.00
     N    3264      7.00
     C   11667      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 744.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4386

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 15 sheets defined
      55.9% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 13
      removed outlier: 3.778A  pdb=" N   LEU B  13 " --> pdb=" O   PRO B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 43
      removed outlier: 3.544A  pdb=" N   ILE B  33 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   ALA B  35 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.845A  pdb=" N   ALA B  49 " --> pdb=" O   GLY B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 59
      removed outlier: 3.526A  pdb=" N   LEU B  59 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 90
      removed outlier: 3.554A  pdb=" N   GLU B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE B  85 " --> pdb=" O   HIS B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 101
    Processing helix  chain 'B' and resid 108 through 119
      removed outlier: 3.701A  pdb=" N   LEU B 115 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ARG B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 124
      removed outlier: 3.687A  pdb=" N   GLU B 123 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 140
    Processing helix  chain 'B' and resid 157 through 173
      removed outlier: 3.608A  pdb=" N   ASP B 166 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR B 173 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 187
      removed outlier: 5.245A  pdb=" N   VAL B 182 " --> pdb=" O   GLU B 178 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B 183 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TRP B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 196
      removed outlier: 3.710A  pdb=" N   ARG B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASP B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.567A  pdb=" N   LEU B 201 " --> pdb=" O   ILE B 197 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 197 through 202'
    Processing helix  chain 'B' and resid 217 through 240
      removed outlier: 3.718A  pdb=" N   THR B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   VAL B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ARG B 237 " --> pdb=" O   LYS B 233 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   ASP B 238 " --> pdb=" O   GLN B 234 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 239 " --> pdb=" O   GLN B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 266
      removed outlier: 3.979A  pdb=" N   LYS B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 281
      removed outlier: 3.859A  pdb=" N   ASN B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.635A  pdb=" N   GLU B 287 " --> pdb=" O   PRO B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 317
      removed outlier: 3.741A  pdb=" N   ILE B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ASP B 314 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 347
      removed outlier: 4.026A  pdb=" N   ALA B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLU B 334 " --> pdb=" O   ARG B 330 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ARG B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 364
      removed outlier: 3.623A  pdb=" N   ALA B 361 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 378
      removed outlier: 3.503A  pdb=" N   ARG B 375 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.658A  pdb=" N   HIS B 402 " --> pdb=" O   ARG B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 437
      removed outlier: 4.356A  pdb=" N   TYR B 430 " --> pdb=" O   ASP B 426 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   SER B 435 " --> pdb=" O   MET B 431 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLU B 436 " --> pdb=" O   LYS B 432 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 460
    Processing helix  chain 'B' and resid 510 through 517
      removed outlier: 3.625A  pdb=" N   TYR B 514 " --> pdb=" O   GLY B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 535
      removed outlier: 4.214A  pdb=" N   CYS B 522 " --> pdb=" O   MET B 518 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 573
      removed outlier: 4.358A  pdb=" N   ALA B 565 " --> pdb=" O   ARG B 561 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN B 566 " --> pdb=" O   GLN B 562 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASP B 569 " --> pdb=" O   ALA B 565 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA B 570 " --> pdb=" O   GLN B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 589
      removed outlier: 3.531A  pdb=" N   GLU B 589 " --> pdb=" O   SER B 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 586 through 589'
    Processing helix  chain 'B' and resid 590 through 605
      removed outlier: 3.975A  pdb=" N   GLN B 594 " --> pdb=" O   THR B 590 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TRP B 598 " --> pdb=" O   GLN B 594 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL B 603 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 617
      removed outlier: 3.679A  pdb=" N   ARG B 613 " --> pdb=" O   GLU B 609 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   SER B 614 " --> pdb=" O   ASN B 610 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ALA B 615 " --> pdb=" O   THR B 611 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU B 616 " --> pdb=" O   LEU B 612 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA B 617 " --> pdb=" O   ARG B 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 634
      removed outlier: 3.801A  pdb=" N   LEU B 631 " --> pdb=" O   ASP B 627 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASN B 633 " --> pdb=" O   GLU B 629 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP B 634 " --> pdb=" O   THR B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 655
      removed outlier: 3.943A  pdb=" N   VAL B 641 " --> pdb=" O   ALA B 637 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL B 642 " --> pdb=" O   TRP B 638 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   GLU B 643 " --> pdb=" O   ASP B 639 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU B 644 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 668
      removed outlier: 3.622A  pdb=" N   ALA B 663 " --> pdb=" O   PRO B 659 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 677
      removed outlier: 3.832A  pdb=" N   THR B 677 " --> pdb=" O   ASN B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 701
      removed outlier: 3.592A  pdb=" N   ARG B 683 " --> pdb=" O   GLY B 679 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR B 685 " --> pdb=" O   GLU B 681 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ASP B 686 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE B 687 " --> pdb=" O   ARG B 683 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU B 688 " --> pdb=" O   LEU B 684 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLN B 695 " --> pdb=" O   SER B 691 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLU B 696 " --> pdb=" O   GLU B 692 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN B 700 " --> pdb=" O   GLU B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 717
      removed outlier: 4.089A  pdb=" N   ARG B 709 " --> pdb=" O   HIS B 705 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 716 " --> pdb=" O   SER B 712 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU B 717 " --> pdb=" O   GLN B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 783 through 805
      removed outlier: 3.548A  pdb=" N   LEU B 789 " --> pdb=" O   GLU B 785 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLU B 793 " --> pdb=" O   LEU B 789 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B 794 " --> pdb=" O   ALA B 790 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU B 799 " --> pdb=" O   LEU B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 835
    Processing helix  chain 'B' and resid 836 through 843
      removed outlier: 3.834A  pdb=" N   ARG B 840 " --> pdb=" O   SER B 836 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B 841 " --> pdb=" O   ALA B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 849 through 860
      removed outlier: 4.441A  pdb=" N   THR B 855 " --> pdb=" O   ALA B 851 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   CYS B 856 " --> pdb=" O   GLY B 852 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LEU B 860 " --> pdb=" O   CYS B 856 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 39 through 55
    Processing helix  chain 'C' and resid 64 through 77
      removed outlier: 3.521A  pdb=" N   ARG C  75 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 103
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'C' and resid 108 through 116
    Processing helix  chain 'C' and resid 121 through 142
    Processing helix  chain 'C' and resid 142 through 152
      removed outlier: 3.809A  pdb=" N   LEU C 146 " --> pdb=" O   ARG C 142 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 179
      Proline residue:  C 167  - end of helix
    Processing helix  chain 'C' and resid 185 through 199
      removed outlier: 3.578A  pdb=" N   ARG C 192 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER C 199 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 232
      removed outlier: 3.675A  pdb=" N   LEU C 224 " --> pdb=" O   PRO C 220 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LYS C 232 " --> pdb=" O   GLN C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 260
      removed outlier: 3.811A  pdb=" N   LEU C 257 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ALA C 258 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS C 259 " --> pdb=" O   ALA C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 283
    Processing helix  chain 'C' and resid 297 through 304
    Processing helix  chain 'C' and resid 304 through 315
    Processing helix  chain 'C' and resid 333 through 345
      removed outlier: 3.546A  pdb=" N   LEU C 345 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 360
    Processing helix  chain 'C' and resid 381 through 400
    Processing helix  chain 'C' and resid 414 through 417
      removed outlier: 3.561A  pdb=" N   SER C 417 " --> pdb=" O   ASP C 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 414 through 417'
    Processing helix  chain 'C' and resid 418 through 429
    Processing helix  chain 'C' and resid 447 through 459
      removed outlier: 3.779A  pdb=" N   LEU C 451 " --> pdb=" O   SER C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 463
    Processing helix  chain 'C' and resid 466 through 475
    Processing helix  chain 'C' and resid 476 through 483
      removed outlier: 3.626A  pdb=" N   PHE C 483 " --> pdb=" O   LEU C 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 486 through 501
      removed outlier: 3.806A  pdb=" N   ARG C 491 " --> pdb=" O   GLU C 487 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR C 492 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY C 501 " --> pdb=" O   VAL C 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 514
      removed outlier: 3.840A  pdb=" N   LEU C 514 " --> pdb=" O   ASN C 510 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 523 through 537
    Processing helix  chain 'C' and resid 558 through 578
      removed outlier: 3.797A  pdb=" N   GLY C 562 " --> pdb=" O   ALA C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 588
    Processing helix  chain 'C' and resid 589 through 599
    Processing helix  chain 'C' and resid 605 through 626
    Processing helix  chain 'C' and resid 633 through 646
      removed outlier: 4.216A  pdb=" N   LEU C 637 " --> pdb=" O   PRO C 633 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 722
      removed outlier: 3.794A  pdb=" N   LEU C 717 " --> pdb=" O   ARG C 713 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 745 through 758
    Processing helix  chain 'C' and resid 768 through 780
    Processing helix  chain 'C' and resid 834 through 843
      removed outlier: 4.128A  pdb=" N   HIS C 843 " --> pdb=" O   ARG C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 843 through 851
    Processing helix  chain 'C' and resid 874 through 889
      removed outlier: 4.723A  pdb=" N   ILE C 880 " --> pdb=" O   SER C 876 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 905
    Processing helix  chain 'C' and resid 910 through 933
      removed outlier: 4.232A  pdb=" N   ARG C 930 " --> pdb=" O   GLN C 926 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 973 through 990
    Processing helix  chain 'C' and resid 1012 through 1033
      removed outlier: 4.021A  pdb=" N   SER C1032 " --> pdb=" O   ARG C1028 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1040 through 1049
    Processing helix  chain 'C' and resid 1060 through 1076
    Processing helix  chain 'C' and resid 1087 through 1094
    Processing helix  chain 'C' and resid 1098 through 1120
      Proline residue:  C1115  - end of helix
    Processing helix  chain 'D' and resid 3 through 13
      removed outlier: 4.211A  pdb=" N   ALA D  10 " --> pdb=" O   GLN D   6 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   VAL D  11 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU D  12 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 29
    Processing helix  chain 'D' and resid 32 through 49
      removed outlier: 3.832A  pdb=" N   THR D  36 " --> pdb=" O   HIS D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 66 through 72
    Processing helix  chain 'D' and resid 80 through 87
    Processing helix  chain 'D' and resid 110 through 127
      removed outlier: 3.836A  pdb=" N   VAL D 126 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ASN D 127 " --> pdb=" O   PHE D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 133 through 145
    Processing helix  chain 'D' and resid 152 through 164
    Processing helix  chain 'D' and resid 176 through 192
    Processing helix  chain 'D' and resid 205 through 223
    Processing helix  chain 'D' and resid 226 through 233
    Processing helix  chain 'D' and resid 240 through 245
    Processing helix  chain 'D' and resid 270 through 274
      removed outlier: 3.664A  pdb=" N   MET D 273 " --> pdb=" O   GLU D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 308 through 315
      removed outlier: 3.816A  pdb=" N   ASP D 312 " --> pdb=" O   ALA D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 320
      removed outlier: 3.627A  pdb=" N   ALA D 319 " --> pdb=" O   TYR D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 334
    Processing helix  chain 'D' and resid 345 through 351
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.911A  pdb=" N   GLU B   6 " --> pdb=" O   HIS B 440 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ALA B 439 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU B  20 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ILE B 383 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL B  61 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152
      removed outlier: 6.778A  pdb=" N   GLN B 151 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.638A  pdb=" N   VAL B 777 " --> pdb=" O   TYR B 768 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR B 768 " --> pdb=" O   VAL B 777 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 491
      removed outlier: 3.709A  pdb=" N   ARG B 488 " --> pdb=" O   MET B 541 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   MET B 541 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL B 490 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502
    Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558
      removed outlier: 3.843A  pdb=" N   VAL B 739 " --> pdb=" O   VAL B 556 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL B 558 " --> pdb=" O   VAL B 739 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL B 579 " --> pdb=" O   ILE B 738 " (cutoff:3.500A)
      removed outlier: 9.295A  pdb=" N   THR B 740 " --> pdb=" O   VAL B 579 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61
      removed outlier: 3.607A  pdb=" N   ASP C  61 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 8.711A  pdb=" N   LEU C 239 " --> pdb=" O   VAL C 211 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   ILE C 213 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ARG C   3 " --> pdb=" O   LEU C 238 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   LEU C   2 " --> pdb=" O   GLN C 321 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   LEU C 323 " --> pdb=" O   LEU C   2 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL C   4 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ARG C 265 " --> pdb=" O   ASP C 324 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN C 264 " --> pdb=" O   ARG C 272 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366
      removed outlier: 6.492A  pdb=" N   ARG C 365 " --> pdb=" O   TYR C 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439
      removed outlier: 6.693A  pdb=" N   ALA C 438 " --> pdb=" O   ILE C 661 " (cutoff:3.500A)
      removed outlier: 8.889A  pdb=" N   THR C 663 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   CYS C 662 " --> pdb=" O   VAL C 410 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS C 676 " --> pdb=" O   ILE C 409 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL C 675 " --> pdb=" O   LYS C 726 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER C 730 " --> pdb=" O   LEU C 677 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   THR C 375 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE C 729 " --> pdb=" O   THR C 375 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR C 731 " --> pdb=" O   HIS C 377 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   CYS C 379 " --> pdb=" O   TYR C 731 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS C 782 " --> pdb=" O   PHE C 376 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443
    Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833
      removed outlier: 3.793A  pdb=" N   THR C 953 " --> pdb=" O   VAL C 832 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   GLN C 951 " --> pdb=" O   CYS C 947 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   CYS C 947 " --> pdb=" O   GLN C 951 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   THR C 953 " --> pdb=" O   LEU C 945 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   LEU C 945 " --> pdb=" O   THR C 953 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   TRP C 955 " --> pdb=" O   ILE C 943 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ILE C 943 " --> pdb=" O   TRP C 955 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET C 941 " --> pdb=" O   PRO C 957 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 963 through 967
      removed outlier: 6.125A  pdb=" N   LEU C 964 " --> pdb=" O   ARG C 997 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   PHE C 999 " --> pdb=" O   LEU C 964 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ARG C 966 " --> pdb=" O   PHE C 999 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   SER C 996 " --> pdb=" O   PHE C1008 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   PHE C1008 " --> pdb=" O   SER C 996 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051
      removed outlier: 3.658A  pdb=" N   ALA C1056 " --> pdb=" O   ASP C1051 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.625A  pdb=" N   LEU D  53 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU D 107 " --> pdb=" O   LEU D  53 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 170
      removed outlier: 6.675A  pdb=" N   SER D 167 " --> pdb=" O   PHE D 294 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   GLY D 296 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE D 169 " --> pdb=" O   GLY D 296 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU D 266 " --> pdb=" O   ILE D 293 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   LEU D 295 " --> pdb=" O   LEU D 266 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL D 268 " --> pdb=" O   LEU D 295 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG D 200 " --> pdb=" O   VAL D 265 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL D 267 " --> pdb=" O   ARG D 200 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA D 202 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
      removed outlier: 9.201A  pdb=" N   SER D 238 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU D 201 " --> pdb=" O   SER D 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6

    802 hydrogen bonds defined for protein.
    2358 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.20

  Time building geometry restraints manager: 2.10 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: 6143
        1.34 -     1.46: 3479
        1.46 -     1.58: 9099
        1.58 -     1.70: 1
        1.70 -     1.82: 143
  Bond restraints: 18865
  Sorted by residual:
  bond pdb=" CA  ASP B 155 "
       pdb=" CB  ASP B 155 "
    ideal  model  delta    sigma   weight residual
    1.526  1.605 -0.079 1.76e-02 3.23e+03 2.02e+01
  bond pdb=" CA  ARG C 433 "
       pdb=" CB  ARG C 433 "
    ideal  model  delta    sigma   weight residual
    1.528  1.552 -0.024 1.39e-02 5.18e+03 2.90e+00
  bond pdb=" CB  GLN B 281 "
       pdb=" CG  GLN B 281 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.32e+00
  bond pdb=" C   LEU D 276 "
       pdb=" N   PRO D 277 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.28e-02 6.10e+03 2.02e+00
  bond pdb=" CG  GLN B 281 "
       pdb=" CD  GLN B 281 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.78e+00
  ... (remaining 18860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 25133
        2.46 -     4.92: 371
        4.92 -     7.38: 78
        7.38 -     9.84: 15
        9.84 -    12.29: 3
  Bond angle restraints: 25600
  Sorted by residual:
  angle pdb=" CA  ARG B 259 "
        pdb=" CB  ARG B 259 "
        pdb=" CG  ARG B 259 "
      ideal   model   delta    sigma   weight residual
     114.10  124.53  -10.43 2.00e+00 2.50e-01 2.72e+01
  angle pdb=" CB  MET B 136 "
        pdb=" CG  MET B 136 "
        pdb=" SD  MET B 136 "
      ideal   model   delta    sigma   weight residual
     112.70  124.99  -12.29 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" C   PHE C 277 "
        pdb=" N   ARG C 278 "
        pdb=" CA  ARG C 278 "
      ideal   model   delta    sigma   weight residual
     122.46  115.16    7.30 1.80e+00 3.09e-01 1.64e+01
  angle pdb=" C   LEU D   8 "
        pdb=" N   GLU D   9 "
        pdb=" CA  GLU D   9 "
      ideal   model   delta    sigma   weight residual
     121.14  114.10    7.04 1.75e+00 3.27e-01 1.62e+01
  angle pdb=" C   ASP B 384 "
        pdb=" N   GLU B 385 "
        pdb=" CA  GLU B 385 "
      ideal   model   delta    sigma   weight residual
     121.54  129.19   -7.65 1.91e+00 2.74e-01 1.61e+01
  ... (remaining 25595 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 10191
       17.99 -    35.97: 1042
       35.97 -    53.96: 163
       53.96 -    71.95: 42
       71.95 -    89.94: 16
  Dihedral angle restraints: 11454
    sinusoidal: 4706
      harmonic: 6748
  Sorted by residual:
  dihedral pdb=" CA  GLN B 417 "
           pdb=" C   GLN B 417 "
           pdb=" N   ALA B 418 "
           pdb=" CA  ALA B 418 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.82   41.18     0      5.00e+00 4.00e-02 6.78e+01
  dihedral pdb=" CA  LEU C 460 "
           pdb=" C   LEU C 460 "
           pdb=" N   PRO C 461 "
           pdb=" CA  PRO C 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.73  -26.27     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ASP B 414 "
           pdb=" C   ASP B 414 "
           pdb=" N   PRO B 415 "
           pdb=" CA  PRO B 415 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.12  -25.88     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 11451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 2266
       0.055 -    0.110: 465
       0.110 -    0.165: 89
       0.165 -    0.220: 8
       0.220 -    0.275: 2
  Chirality restraints: 2830
  Sorted by residual:
  chirality pdb=" CB  THR C 402 "
            pdb=" CA  THR C 402 "
            pdb=" OG1 THR C 402 "
            pdb=" CG2 THR C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  ARG B 259 "
            pdb=" N   ARG B 259 "
            pdb=" C   ARG B 259 "
            pdb=" CB  ARG B 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CB  ILE C 557 "
            pdb=" CA  ILE C 557 "
            pdb=" CG1 ILE C 557 "
            pdb=" CG2 ILE C 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 2827 not shown)

  Planarity restraints: 3370
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D  65 "   -0.059 5.00e-02 4.00e+02   9.04e-02 1.31e+01
        pdb=" N   PRO D  66 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D  66 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO D  66 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 657 "   -0.047 5.00e-02 4.00e+02   7.17e-02 8.22e+00
        pdb=" N   PRO C 658 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO C 658 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 658 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 259 "    0.219 9.50e-02 1.11e+02   9.86e-02 7.18e+00
        pdb=" NE  ARG B 259 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 259 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 259 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 259 "    0.001 2.00e-02 2.50e+03
  ... (remaining 3367 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3178
        2.77 -     3.30: 17185
        3.30 -     3.83: 29823
        3.83 -     4.37: 31373
        4.37 -     4.90: 53838
  Nonbonded interactions: 135397
  Sorted by model distance:
  nonbonded pdb=" O   SER B  24 "
            pdb=" OG1 THR B  27 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ALA D 159 "
            pdb=" OG1 THR D 163 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   PHE B 386 "
            pdb=" OG1 THR B 389 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OD1 ASP C1060 "
            pdb=" OG1 THR C1063 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   LYS C  94 "
            pdb=" OG1 THR C  97 "
     model   vdw
     2.296 3.040
  ... (remaining 135392 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.590
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
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   0.079  18865  Z= 0.161
  Angle     :  0.784  12.294  25600  Z= 0.406
  Chirality :  0.047   0.275   2830
  Planarity :  0.006   0.099   3370
  Dihedral  : 14.913  89.936   7068
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.46 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.16), residues: 2306
  helix: -0.34 (0.14), residues: 1148
  sheet: -0.65 (0.43), residues: 157
  loop : -2.27 (0.18), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 259 
 TYR   0.033   0.002   TYR C 190 
 PHE   0.040   0.002   PHE C  73 
 TRP   0.020   0.001   TRP B 447 
 HIS   0.008   0.001   HIS D 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (18865)
  covalent geometry    : angle       0.78445 (25600)
  hydrogen bonds       : bond        0.14161 (  802)
  hydrogen bonds       : angle       5.23827 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.759 
Fit side-chains
REVERT: B  453 MET cc_start: 0.8857 (mmm) cc_final: 0.8448 (mmt)
REVERT: B  469 MET cc_start: 0.8679 (mmm) cc_final: 0.8462 (mmm)
REVERT: B  509 CYS cc_start: 0.6816 (p) cc_final: 0.6508 (p)
REVERT: B  621 MET cc_start: 0.8552 (tpt) cc_final: 0.8347 (mmm)
REVERT: C  190 TYR cc_start: 0.8034 (p90) cc_final: 0.7808 (p90)
REVERT: C  396 MET cc_start: 0.8560 (mtm) cc_final: 0.8008 (mtt)
REVERT: C  537 MET cc_start: 0.8696 (ptp) cc_final: 0.8431 (ptp)
REVERT: C  787 MET cc_start: 0.8985 (mmp) cc_final: 0.8476 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1199
  time to fit residues: 23.7270
Evaluate side-chains
  94 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 216 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    7.9990
   chunk 227 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 200 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
B 258 ASN
B 689 HIS
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 765 GLN
C 510 ASN
D 110 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.066076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055198 restraints weight = 119673.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.056451 restraints weight = 72456.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.057224 restraints weight = 50855.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.057833 restraints weight = 39741.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.058248 restraints weight = 33255.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18865  Z= 0.201
  Angle     :  0.615  11.477  25600  Z= 0.319
  Chirality :  0.041   0.155   2830
  Planarity :  0.005   0.079   3370
  Dihedral  :  4.950  41.761   2540
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.85 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.17), residues: 2306
  helix:  0.45 (0.15), residues: 1168
  sheet: -0.62 (0.42), residues: 152
  loop : -2.21 (0.18), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 259 
 TYR   0.014   0.001   TYR C1027 
 PHE   0.018   0.002   PHE C  73 
 TRP   0.014   0.001   TRP B 447 
 HIS   0.005   0.001   HIS B 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (18865)
  covalent geometry    : angle       0.61500 (25600)
  hydrogen bonds       : bond        0.04972 (  802)
  hydrogen bonds       : angle       4.63113 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 LEU cc_start: 0.9374 (tp) cc_final: 0.9170 (tt)
REVERT: B  509 CYS cc_start: 0.6580 (p) cc_final: 0.6289 (p)
REVERT: B  620 MET cc_start: 0.8608 (tpt) cc_final: 0.8335 (tpt)
REVERT: C  396 MET cc_start: 0.8370 (mtm) cc_final: 0.7920 (mtt)
REVERT: C  537 MET cc_start: 0.8607 (ptp) cc_final: 0.8350 (ptp)
REVERT: C  667 MET cc_start: 0.4082 (mmm) cc_final: 0.3459 (mmm)
REVERT: C  680 MET cc_start: 0.9100 (mmm) cc_final: 0.8842 (mmm)
REVERT: D  270 GLU cc_start: 0.8526 (tp30) cc_final: 0.8325 (tp30)
REVERT: D  273 MET cc_start: 0.7893 (mtt) cc_final: 0.7309 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1170
  time to fit residues: 22.3186
Evaluate side-chains
  84 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 189 optimal weight:    9.9990
   chunk 177 optimal weight:   20.0000
   chunk 123 optimal weight:    2.9990
   chunk 219 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 213 optimal weight:    8.9990
   chunk 187 optimal weight:    0.8980
   chunk 145 optimal weight:   10.0000
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 834 HIS
B 835 GLN
C 233 HIS
C 510 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.061792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.051726 restraints weight = 109906.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.053024 restraints weight = 64652.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.053907 restraints weight = 44491.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.054495 restraints weight = 33978.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.054880 restraints weight = 28066.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  18865  Z= 0.106
  Angle     :  0.528  13.945  25600  Z= 0.271
  Chirality :  0.040   0.189   2830
  Planarity :  0.004   0.079   3370
  Dihedral  :  4.602  39.129   2540
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.17), residues: 2306
  helix:  0.88 (0.15), residues: 1160
  sheet: -0.38 (0.45), residues: 146
  loop : -2.06 (0.18), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 306 
 TYR   0.010   0.001   TYR C1027 
 PHE   0.013   0.001   PHE C  73 
 TRP   0.012   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (18865)
  covalent geometry    : angle       0.52825 (25600)
  hydrogen bonds       : bond        0.04052 (  802)
  hydrogen bonds       : angle       4.22249 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  509 CYS cc_start: 0.6644 (p) cc_final: 0.6326 (p)
REVERT: C  396 MET cc_start: 0.8433 (mtm) cc_final: 0.7922 (mtt)
REVERT: C  680 MET cc_start: 0.9178 (mmm) cc_final: 0.8940 (mmm)
REVERT: D  270 GLU cc_start: 0.8531 (tp30) cc_final: 0.8157 (tp30)
REVERT: D  273 MET cc_start: 0.7984 (mtt) cc_final: 0.7359 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1275
  time to fit residues: 25.8068
Evaluate side-chains
  91 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 134 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 164 optimal weight:    0.3980
   chunk 27 optimal weight:   10.0000
   chunk 220 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 167 optimal weight:    3.9990
   chunk 48 optimal weight:   20.0000
   chunk 190 optimal weight:    0.0470
   chunk 60 optimal weight:    9.9990
   overall best weight:    2.0884

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

Flipped N/Q/H residues before XYZ refinement:
B 531 GLN
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 739 ASN
C 979 GLN
D 110 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.067745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.056982 restraints weight = 119197.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.058251 restraints weight = 71576.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.059078 restraints weight = 49784.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.059664 restraints weight = 38795.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.060047 restraints weight = 32220.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18865  Z= 0.122
  Angle     :  0.531  13.839  25600  Z= 0.272
  Chirality :  0.040   0.210   2830
  Planarity :  0.004   0.077   3370
  Dihedral  :  4.524  42.110   2540
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.85 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.04 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.18), residues: 2306
  helix:  0.95 (0.15), residues: 1176
  sheet: -0.38 (0.45), residues: 146
  loop : -2.05 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 808 
 TYR   0.025   0.001   TYR C 190 
 PHE   0.011   0.001   PHE B 386 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (18865)
  covalent geometry    : angle       0.53145 (25600)
  hydrogen bonds       : bond        0.03951 (  802)
  hydrogen bonds       : angle       4.18190 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: B  509 CYS cc_start: 0.6690 (p) cc_final: 0.6353 (p)
REVERT: C  190 TYR cc_start: 0.7479 (p90) cc_final: 0.6764 (p90)
REVERT: C  396 MET cc_start: 0.8313 (mtm) cc_final: 0.7818 (mtt)
REVERT: C 1031 MET cc_start: 0.7571 (ptp) cc_final: 0.7173 (ptp)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1243
  time to fit residues: 23.2594
Evaluate side-chains
  87 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 114 optimal weight:    8.9990
   chunk 139 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0570
   chunk 141 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 121 optimal weight:    2.9990
   chunk 186 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 180 optimal weight:    0.0870
   overall best weight:    1.4280

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

Flipped N/Q/H residues before XYZ refinement:
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 228 GLN
C 510 ASN
C 739 ASN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.062305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.052125 restraints weight = 108706.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.053391 restraints weight = 65215.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.054242 restraints weight = 45495.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.054812 restraints weight = 35243.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.055182 restraints weight = 29407.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  18865  Z= 0.102
  Angle     :  0.520  14.093  25600  Z= 0.264
  Chirality :  0.040   0.180   2830
  Planarity :  0.004   0.079   3370
  Dihedral  :  4.395  39.709   2540
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.13 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.18), residues: 2306
  helix:  1.17 (0.16), residues: 1171
  sheet: -0.29 (0.45), residues: 147
  loop : -2.00 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 255 
 TYR   0.022   0.001   TYR C 190 
 PHE   0.014   0.001   PHE C 901 
 TRP   0.022   0.001   TRP B 187 
 HIS   0.003   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (18865)
  covalent geometry    : angle       0.52003 (25600)
  hydrogen bonds       : bond        0.03680 (  802)
  hydrogen bonds       : angle       4.03264 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 MET cc_start: 0.8508 (mmm) cc_final: 0.8282 (mmp)
REVERT: B  509 CYS cc_start: 0.6827 (p) cc_final: 0.6492 (p)
REVERT: C  190 TYR cc_start: 0.7583 (p90) cc_final: 0.6831 (p90)
REVERT: C  396 MET cc_start: 0.8371 (mtm) cc_final: 0.7847 (mtt)
REVERT: C  667 MET cc_start: 0.4138 (mmt) cc_final: 0.3139 (mmm)
REVERT: C  924 MET cc_start: 0.7786 (mmp) cc_final: 0.7428 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1311
  time to fit residues: 25.0094
Evaluate side-chains
  93 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 145 optimal weight:    0.8980
   chunk 185 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0370
   chunk 42 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 221 optimal weight:   10.0000
   chunk 133 optimal weight:    9.9990
   chunk 222 optimal weight:    6.9990
   overall best weight:    3.1864

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

Flipped N/Q/H residues before XYZ refinement:
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 699 GLN
C 739 ASN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.066555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.055723 restraints weight = 119634.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.056960 restraints weight = 72036.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.057787 restraints weight = 50336.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.058305 restraints weight = 39006.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.058746 restraints weight = 32884.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  18865  Z= 0.168
  Angle     :  0.577  14.449  25600  Z= 0.294
  Chirality :  0.041   0.159   2830
  Planarity :  0.004   0.074   3370
  Dihedral  :  4.548  40.113   2540
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.85 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.38 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.18), residues: 2306
  helix:  1.08 (0.15), residues: 1177
  sheet: -0.62 (0.43), residues: 156
  loop : -2.09 (0.19), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 259 
 TYR   0.017   0.001   TYR C 190 
 PHE   0.013   0.001   PHE D 123 
 TRP   0.022   0.001   TRP B 187 
 HIS   0.005   0.001   HIS C 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (18865)
  covalent geometry    : angle       0.57691 (25600)
  hydrogen bonds       : bond        0.04174 (  802)
  hydrogen bonds       : angle       4.26097 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 MET cc_start: 0.8490 (mmm) cc_final: 0.8222 (mmp)
REVERT: C  190 TYR cc_start: 0.7520 (p90) cc_final: 0.6794 (p90)
REVERT: C  396 MET cc_start: 0.8251 (mtm) cc_final: 0.7837 (mtt)
REVERT: C  594 MET cc_start: 0.8884 (tpp) cc_final: 0.8637 (mmt)
REVERT: C 1031 MET cc_start: 0.7478 (ptp) cc_final: 0.7068 (ptp)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1337
  time to fit residues: 24.6789
Evaluate side-chains
  85 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 222 optimal weight:    0.3980
   chunk 114 optimal weight:    0.3980
   chunk 40 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 163 optimal weight:    9.9990
   chunk 169 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0570
   chunk 160 optimal weight:    4.9990
   chunk 172 optimal weight:    8.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.7702

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

Flipped N/Q/H residues before XYZ refinement:
B 632 ASN
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 739 ASN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.061393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.051574 restraints weight = 109310.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.052816 restraints weight = 64648.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.053662 restraints weight = 44702.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.054248 restraints weight = 34280.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.054652 restraints weight = 28259.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  18865  Z= 0.111
  Angle     :  0.531  14.959  25600  Z= 0.270
  Chirality :  0.040   0.210   2830
  Planarity :  0.004   0.076   3370
  Dihedral  :  4.430  38.279   2540
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.08 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.18), residues: 2306
  helix:  1.24 (0.16), residues: 1175
  sheet: -0.43 (0.44), residues: 148
  loop : -1.99 (0.19), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 259 
 TYR   0.021   0.001   TYR C 190 
 PHE   0.010   0.001   PHE D 123 
 TRP   0.022   0.001   TRP B 811 
 HIS   0.003   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (18865)
  covalent geometry    : angle       0.53106 (25600)
  hydrogen bonds       : bond        0.03787 (  802)
  hydrogen bonds       : angle       4.04919 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: B  501 MET cc_start: 0.8616 (ppp) cc_final: 0.8328 (ppp)
REVERT: C  190 TYR cc_start: 0.7677 (p90) cc_final: 0.6899 (p90)
REVERT: C  396 MET cc_start: 0.8380 (mtm) cc_final: 0.7848 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1222
  time to fit residues: 22.9067
Evaluate side-chains
  88 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 186 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 125 optimal weight:    0.4980
   chunk 115 optimal weight:    0.9980
   chunk 222 optimal weight:    0.6980
   chunk 226 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0670
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 739 ASN
C 881 ASN
C 920 GLN
D 110 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.069570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.058719 restraints weight = 117504.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.060027 restraints weight = 69519.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.060890 restraints weight = 48023.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.061433 restraints weight = 36845.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.061887 restraints weight = 30784.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  18865  Z= 0.092
  Angle     :  0.539  13.999  25600  Z= 0.268
  Chirality :  0.040   0.185   2830
  Planarity :  0.004   0.075   3370
  Dihedral  :  4.265  36.312   2540
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.17 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.18), residues: 2306
  helix:  1.32 (0.16), residues: 1176
  sheet: -0.16 (0.44), residues: 147
  loop : -1.91 (0.19), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 445 
 TYR   0.021   0.001   TYR C 190 
 PHE   0.008   0.001   PHE C 694 
 TRP   0.022   0.001   TRP B 187 
 HIS   0.003   0.000   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (18865)
  covalent geometry    : angle       0.53909 (25600)
  hydrogen bonds       : bond        0.03428 (  802)
  hydrogen bonds       : angle       3.92641 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 MET cc_start: 0.8518 (mmm) cc_final: 0.8294 (mmp)
REVERT: B  501 MET cc_start: 0.8724 (ppp) cc_final: 0.8357 (ppp)
REVERT: C  190 TYR cc_start: 0.7775 (p90) cc_final: 0.6893 (p90)
REVERT: C  396 MET cc_start: 0.8411 (mtm) cc_final: 0.7845 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1163
  time to fit residues: 24.3020
Evaluate side-chains
  92 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 186 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   chunk 125 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    9.9990
   chunk 175 optimal weight:    3.9990
   chunk 153 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 126 optimal weight:    2.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 739 ASN
D 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.061701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.051886 restraints weight = 108746.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.053124 restraints weight = 64404.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.053970 restraints weight = 44619.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.054543 restraints weight = 34206.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.054900 restraints weight = 28309.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  18865  Z= 0.119
  Angle     :  0.559  13.795  25600  Z= 0.278
  Chirality :  0.040   0.194   2830
  Planarity :  0.004   0.074   3370
  Dihedral  :  4.312  36.346   2540
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.86 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.18), residues: 2306
  helix:  1.28 (0.16), residues: 1183
  sheet: -0.20 (0.45), residues: 148
  loop : -1.89 (0.19), residues: 975

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 259 
 TYR   0.018   0.001   TYR C 190 
 PHE   0.011   0.001   PHE D 123 
 TRP   0.024   0.001   TRP B 187 
 HIS   0.003   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (18865)
  covalent geometry    : angle       0.55927 (25600)
  hydrogen bonds       : bond        0.03651 (  802)
  hydrogen bonds       : angle       4.02763 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: B  469 MET cc_start: 0.8467 (mmm) cc_final: 0.8241 (mmp)
REVERT: B  501 MET cc_start: 0.8643 (ppp) cc_final: 0.8311 (ppp)
REVERT: C  190 TYR cc_start: 0.7677 (p90) cc_final: 0.6894 (p90)
REVERT: C  396 MET cc_start: 0.8318 (mtm) cc_final: 0.7821 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1138
  time to fit residues: 22.1287
Evaluate side-chains
  92 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 195 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 212 optimal weight:    5.9990
   chunk 152 optimal weight:    8.9990
   chunk 108 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 155 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
C 817 HIS
D 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.067028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.056232 restraints weight = 118807.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.057478 restraints weight = 71077.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.058255 restraints weight = 49817.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.058854 restraints weight = 38986.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.059186 restraints weight = 32566.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18865  Z= 0.154
  Angle     :  0.597  14.437  25600  Z= 0.298
  Chirality :  0.041   0.196   2830
  Planarity :  0.004   0.073   3370
  Dihedral  :  4.489  36.724   2540
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.46 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.18), residues: 2306
  helix:  1.23 (0.16), residues: 1177
  sheet: -0.24 (0.45), residues: 142
  loop : -1.93 (0.19), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 259 
 TYR   0.016   0.001   TYR C 190 
 PHE   0.023   0.001   PHE D 123 
 TRP   0.020   0.001   TRP C 504 
 HIS   0.004   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (18865)
  covalent geometry    : angle       0.59682 (25600)
  hydrogen bonds       : bond        0.04028 (  802)
  hydrogen bonds       : angle       4.20635 ( 2358)

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

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

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4612 Ramachandran restraints generated.
    2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: B  469 MET cc_start: 0.8557 (mmm) cc_final: 0.8317 (mmp)
REVERT: B  501 MET cc_start: 0.8838 (ppp) cc_final: 0.8365 (ppp)
REVERT: C  190 TYR cc_start: 0.7805 (p90) cc_final: 0.6972 (p90)
REVERT: C  396 MET cc_start: 0.8391 (mtm) cc_final: 0.7891 (mtt)
REVERT: D  273 MET cc_start: 0.7744 (mtt) cc_final: 0.7354 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1218
  time to fit residues: 22.0309
Evaluate side-chains
  89 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0000
   chunk 57 optimal weight:    4.9990
   chunk 175 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 219 optimal weight:    0.0000
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 HIS
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 510 ASN
D 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.068319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.057615 restraints weight = 118741.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.058899 restraints weight = 70754.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.059743 restraints weight = 49174.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.060315 restraints weight = 38076.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.060746 restraints weight = 31691.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  18865  Z= 0.104
  Angle     :  0.565  14.541  25600  Z= 0.279
  Chirality :  0.041   0.276   2830
  Planarity :  0.004   0.075   3370
  Dihedral  :  4.378  35.720   2540
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.18), residues: 2306
  helix:  1.29 (0.16), residues: 1179
  sheet: -0.23 (0.44), residues: 147
  loop : -1.88 (0.19), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 259 
 TYR   0.020   0.001   TYR C 190 
 PHE   0.023   0.001   PHE C 901 
 TRP   0.017   0.001   TRP B 187 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (18865)
  covalent geometry    : angle       0.56534 (25600)
  hydrogen bonds       : bond        0.03699 (  802)
  hydrogen bonds       : angle       4.04413 ( 2358)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2521.12 seconds
wall clock time: 44 minutes 30.57 seconds (2670.57 seconds total)