Starting phenix.real_space_refine
on Thu Dec  7 22:05:35 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctg_26989/12_2023/8ctg_26989_updated.pdb"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.035
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      45      5.16       5
     C    3041      2.51       5
     N    1006      2.21       5
     O    1008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 5100
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 618
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 343
          Unresolved non-hydrogen angles: 440
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 222
    Chain: "B"
      Number of atoms: 1585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 1585
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 241}
          Link IDs: {'PTRANS': 4, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 908
          Unresolved non-hydrogen angles: 1156
          Unresolved non-hydrogen dihedrals: 769
          Unresolved non-hydrogen chiralities: 70
          Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 14, 'TYR:plan': 5, 'ASN:plan1': 18, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 21, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 541
    Chain: "C"
      Number of atoms: 2880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 2880
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 456}
          Link IDs: {'PTRANS': 24, 'TRANS': 547}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1778
          Unresolved non-hydrogen angles: 2320
          Unresolved non-hydrogen dihedrals: 1490
          Unresolved non-hydrogen chiralities: 166
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 12, 'TYR:plan': 21, 'ASN:plan1': 22, 'TRP:plan': 19, 'ASP:plan': 51, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 37}
          Unresolved non-hydrogen planarities: 1084
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 69
    residue:
      pdb=" N   LEU A  97 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU A  97 " occ=0.20
    residue:
      pdb=" N   GLU A  98 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLU A  98 " occ=0.20
    residue:
      pdb=" N   ASP A  99 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  ASP A  99 " occ=0.20
    residue:
      pdb=" N   TYR A 100 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  TYR A 100 " occ=0.20
    residue:
      pdb=" N   LYS A 101 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LYS A 101 " occ=0.20
    residue:
      pdb=" N   PRO B  67 " occ=0.20
      ... (5 atoms not shown)
      pdb=" CD  PRO B  67 " occ=0.20
    residue:
      pdb=" N   GLU B  68 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLU B  68 " occ=0.20
    residue:
      pdb=" N   SER B  69 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  SER B  69 " occ=0.20
    residue:
      pdb=" N   THR B  70 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  THR B  70 " occ=0.20
    residue:
      pdb=" N   LEU B  71 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU B  71 " occ=0.20
    residue:
      pdb=" N   GLN B  72 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLN B  72 " occ=0.20
    residue:
      pdb=" N   LEU B  73 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU B  73 " occ=0.20
    ... (remaining 57 not shown)
  Time building chain proxies: 3.87, per 1000 atoms: 0.76
  Number of scatterers: 5100
  At special positions: 0
  Unit cell: (69.0201, 97.9915, 134.632, 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      45     16.00
     O    1008      8.00
     N    1006      7.00
     C    3041      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 135 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 105 " - pdb=" SG  CYS B 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 115 " - pdb=" SG  CYS B 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 181 " - pdb=" SG  CYS B 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 183 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 260 " - pdb=" SG  CYS B 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 295 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 328 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 315 " - pdb=" SG  CYS B 325 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 320 " - pdb=" SG  CYS B 321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 286 " - pdb=" SG  CYS C 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 293 " - pdb=" SG  CYS C 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 310 " - pdb=" SG  CYS C 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 592 " - pdb=" SG  CYS C 603 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 599 " - pdb=" SG  CYS C 612 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1862

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      20 helices and 15 sheets defined
      18.8% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 43
      No H-bonds generated for 'chain 'A' and resid 41 through 43'
    Processing helix  chain 'A' and resid 62 through 78
      removed outlier: 4.242A  pdb=" N   GLN A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   PHE A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   TRP A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      Proline residue:  A  74  - end of helix
    Processing helix  chain 'A' and resid 82 through 92
      removed outlier: 4.518A  pdb=" N   PHE A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 124
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'B' and resid 38 through 58
      removed outlier: 4.288A  pdb=" N   ALA B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   SER B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 84 through 106
      removed outlier: 3.750A  pdb=" N   PHE B  88 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
      removed outlier: 5.995A  pdb=" N   ASN B 112 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 151
      removed outlier: 3.740A  pdb=" N   GLY B 150 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 175
    Processing helix  chain 'B' and resid 186 through 188
      No H-bonds generated for 'chain 'B' and resid 186 through 188'
    Processing helix  chain 'B' and resid 202 through 214
    Processing helix  chain 'B' and resid 238 through 243
      removed outlier: 3.683A  pdb=" N   SER B 243 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
      removed outlier: 4.118A  pdb=" N   CYS B 291 " --> pdb=" O   GLU B 287 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LYS B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 298
      No H-bonds generated for 'chain 'B' and resid 296 through 298'
    Processing helix  chain 'C' and resid 276 through 278
      No H-bonds generated for 'chain 'C' and resid 276 through 278'
    Processing helix  chain 'C' and resid 290 through 292
      No H-bonds generated for 'chain 'C' and resid 290 through 292'
    Processing helix  chain 'C' and resid 591 through 593
      No H-bonds generated for 'chain 'C' and resid 591 through 593'
    Processing helix  chain 'C' and resid 595 through 598
    Processing sheet with id=  A, first strand: chain 'B' and resid 128 through 130
      removed outlier: 6.367A  pdb=" N   GLN B 193 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'C' and resid 31 through 34
      removed outlier: 3.840A  pdb=" N   ARG C  32 " --> pdb=" O   TYR C  25 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 53 through 59
      removed outlier: 6.176A  pdb=" N   SER C  68 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL C  56 " --> pdb=" O   TYR C  66 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TYR C  66 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE C  58 " --> pdb=" O   LEU C  64 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU C  64 " --> pdb=" O   PHE C  58 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ARG C  77 " --> pdb=" O   ASN C  88 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   ASN C  88 " --> pdb=" O   ARG C  77 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'C' and resid 97 through 103
      removed outlier: 6.632A  pdb=" N   THR C 112 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LEU C 100 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR C 110 " --> pdb=" O   LEU C 100 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   CYS C 102 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   LYS C 108 " --> pdb=" O   CYS C 102 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG C 118 " --> pdb=" O   ASP C 113 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   VAL C 121 " --> pdb=" O   VAL C 131 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   VAL C 131 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'C' and resid 143 through 146
      removed outlier: 6.394A  pdb=" N   ARG C 165 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   ILE C 175 " --> pdb=" O   ARG C 165 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 188 through 190
      removed outlier: 3.970A  pdb=" N   PHE C 205 " --> pdb=" O   ASP C 200 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE C 206 " --> pdb=" O   GLN C 217 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 230 through 232
      removed outlier: 3.669A  pdb=" N   THR C 231 " --> pdb=" O   TYR C 238 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR C 238 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   HIS C 262 " --> pdb=" O   ILE C 247 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ALA C 249 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   GLU C 260 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 296 through 299
    Processing sheet with id=  I, first strand: chain 'C' and resid 578 through 582
      removed outlier: 3.895A  pdb=" N   LYS C 579 " --> pdb=" O   LEU C 332 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU C 332 " --> pdb=" O   LYS C 579 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR C 581 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU C 330 " --> pdb=" O   THR C 581 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE C 342 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'C' and resid 365 through 368
      removed outlier: 3.601A  pdb=" N   VAL C 398 " --> pdb=" O   ILE C 384 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ARG C 386 " --> pdb=" O   PHE C 396 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   PHE C 396 " --> pdb=" O   ARG C 386 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 407 through 411
      removed outlier: 6.162A  pdb=" N   VAL C 429 " --> pdb=" O   ILE C 439 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ILE C 439 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'C' and resid 451 through 454
      removed outlier: 6.240A  pdb=" N   ARG C 473 " --> pdb=" O   VAL C 483 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   VAL C 483 " --> pdb=" O   ARG C 473 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'C' and resid 492 through 498
      removed outlier: 6.514A  pdb=" N   GLY C 507 " --> pdb=" O   ASN C 493 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   LEU C 495 " --> pdb=" O   TYR C 505 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TYR C 505 " --> pdb=" O   LEU C 495 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   LEU C 497 " --> pdb=" O   LYS C 503 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LYS C 503 " --> pdb=" O   LEU C 497 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS C 513 " --> pdb=" O   ASP C 508 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   VAL C 516 " --> pdb=" O   VAL C 526 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   VAL C 526 " --> pdb=" O   VAL C 516 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'C' and resid 539 through 541
      removed outlier: 3.657A  pdb=" N   TYR C 544 " --> pdb=" O   LEU C 541 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ARG C 557 " --> pdb=" O   VAL C 567 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   VAL C 567 " --> pdb=" O   ARG C 557 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   HIS C 559 " --> pdb=" O   ARG C 565 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ARG C 565 " --> pdb=" O   HIS C 559 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'C' and resid 602 through 606

    227 hydrogen bonds defined for protein.
    600 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: 1.87

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 1888
        1.34 -     1.47: 1123
        1.47 -     1.60: 2078
        1.60 -     1.74: 0
        1.74 -     1.87: 45
  Bond restraints: 5134
  Sorted by residual:
  bond pdb=" C   LYS C 303 "
       pdb=" N   PRO C 304 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 2.34e-02 1.83e+03 7.19e+00
  bond pdb=" C1  PAM B 401 "
       pdb=" O1  PAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.250  1.202  0.048 2.00e-02 2.50e+03 5.86e+00
  bond pdb=" CB  CYS B 321 "
       pdb=" SG  CYS B 321 "
    ideal  model  delta    sigma   weight residual
    1.808  1.873 -0.065 3.30e-02 9.18e+02 3.88e+00
  bond pdb=" CB  SER B 187 "
       pdb=" OG  SER B 187 "
    ideal  model  delta    sigma   weight residual
    1.417  1.451 -0.034 2.00e-02 2.50e+03 2.82e+00
  bond pdb=" C1  PAM B 401 "
       pdb=" C2  PAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.538  1.504  0.034 2.00e-02 2.50e+03 2.81e+00
  ... (remaining 5129 not shown)

  Histogram of bond angle deviations from ideal:
      101.48 -   107.75: 251
      107.75 -   114.02: 2754
      114.02 -   120.29: 1593
      120.29 -   126.56: 2503
      126.56 -   132.83: 37
  Bond angle restraints: 7138
  Sorted by residual:
  angle pdb=" C   GLY B 114 "
        pdb=" N   CYS B 115 "
        pdb=" CA  CYS B 115 "
      ideal   model   delta    sigma   weight residual
     121.54  129.52   -7.98 1.91e+00 2.74e-01 1.74e+01
  angle pdb=" CA  ARG C 141 "
        pdb=" C   ARG C 141 "
        pdb=" N   ALA C 142 "
      ideal   model   delta    sigma   weight residual
     119.56  117.20    2.36 5.80e-01 2.97e+00 1.65e+01
  angle pdb=" N   VAL C 381 "
        pdb=" CA  VAL C 381 "
        pdb=" C   VAL C 381 "
      ideal   model   delta    sigma   weight residual
     112.04  107.30    4.74 1.40e+00 5.10e-01 1.14e+01
  angle pdb=" CA  LYS C 303 "
        pdb=" C   LYS C 303 "
        pdb=" N   PRO C 304 "
      ideal   model   delta    sigma   weight residual
     118.44  123.77   -5.33 1.59e+00 3.96e-01 1.12e+01
  angle pdb=" N   SER C 179 "
        pdb=" CA  SER C 179 "
        pdb=" C   SER C 179 "
      ideal   model   delta    sigma   weight residual
     108.67  113.78   -5.11 1.55e+00 4.16e-01 1.09e+01
  ... (remaining 7133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.04: 2980
       12.04 -    24.08: 84
       24.08 -    36.13: 23
       36.13 -    48.17: 10
       48.17 -    60.21: 10
  Dihedral angle restraints: 3107
    sinusoidal: 245
      harmonic: 2862
  Sorted by residual:
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 328 "
           pdb=" CB  CYS B 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.41   55.59     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CB  CYS B 105 "
           pdb=" SG  CYS B 105 "
           pdb=" SG  CYS B 113 "
           pdb=" CB  CYS B 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.59   52.59     1      1.00e+01 1.00e-02 3.77e+01
  dihedral pdb=" CA  CYS B 320 "
           pdb=" C   CYS B 320 "
           pdb=" N   CYS B 321 "
           pdb=" CA  CYS B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.06   20.94     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 3104 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 567
       0.036 -    0.072: 252
       0.072 -    0.108: 73
       0.108 -    0.144: 37
       0.144 -    0.180: 2
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CA  CYS B 321 "
            pdb=" N   CYS B 321 "
            pdb=" C   CYS B 321 "
            pdb=" CB  CYS B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  CYS B 115 "
            pdb=" N   CYS B 115 "
            pdb=" C   CYS B 115 "
            pdb=" CB  CYS B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 928 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 145 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.45e+00
        pdb=" C   LYS B 145 "    0.047 2.00e-02 2.50e+03
        pdb=" O   LYS B 145 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 146 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  72 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   GLN B  72 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLN B  72 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU B  73 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 267 "    0.038 5.00e-02 4.00e+02   5.68e-02 5.16e+00
        pdb=" N   PRO C 268 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 268 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 268 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 600
        2.74 -     3.28: 5077
        3.28 -     3.82: 7607
        3.82 -     4.36: 7542
        4.36 -     4.90: 13477
  Nonbonded interactions: 34303
  Sorted by model distance:
  nonbonded pdb=" O   MET A 122 "
            pdb=" N   PHE A 127 "
     model   vdw
     2.201 2.520
  nonbonded pdb=" O   LYS B 292 "
            pdb=" N   ASP B 297 "
     model   vdw
     2.208 2.520
  nonbonded pdb=" O   SER C  96 "
            pdb=" N   SER C 114 "
     model   vdw
     2.268 2.520
  nonbonded pdb=" N   VAL C 121 "
            pdb=" O   LYS C 130 "
     model   vdw
     2.281 2.520
  nonbonded pdb=" O   CYS B 320 "
            pdb=" N   THR B 322 "
     model   vdw
     2.292 2.520
  ... (remaining 34298 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.20 max=1.00 mean=0.95
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:             1.980
  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:             0.000
  Extract box with map and model:          8.720
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     20.940
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3443
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      :  0.004   0.069   5134  Z= 0.290
  Angle     :  0.978   8.505   7138  Z= 0.582
  Chirality :  0.047   0.180    931
  Planarity :  0.006   0.057   1040
  Dihedral  :  7.618  54.388   1182
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  1.81 %
    Allowed  :  9.66 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  :  8.05 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.23), residues: 994
  helix: -1.41 (0.35), residues: 170
  sheet: -1.53 (0.30), residues: 238
  loop : -2.51 (0.22), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0584
  time to fit residues: 4.4799
Evaluate side-chains
  28 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.549 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 3
  average time/residue: 0.0488
  time to fit residues: 1.0476
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    0.4980
   chunk 77 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0010
   chunk 47 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3527
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   5134  Z= 0.223
  Angle     :  0.633   7.248   7138  Z= 0.350
  Chirality :  0.045   0.152    931
  Planarity :  0.005   0.053   1040
  Dihedral  :  5.704  44.544   1013
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.04 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 14.94 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.25), residues: 994
  helix:  0.53 (0.41), residues: 172
  sheet: -1.52 (0.28), residues: 266
  loop : -1.99 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0526
  time to fit residues: 3.4830
Evaluate side-chains
  25 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.563 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 2
  average time/residue: 0.0475
  time to fit residues: 0.9545
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0040
   chunk 74 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0270
   chunk 24 optimal weight:    0.3980
   chunk 90 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 80 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0370
   chunk 30 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.2528

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3528
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5134  Z= 0.150
  Angle     :  0.526   6.274   7138  Z= 0.284
  Chirality :  0.044   0.130    931
  Planarity :  0.004   0.069   1040
  Dihedral  :  4.682  40.737   1013
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.14 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  :  9.20 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.26), residues: 994
  helix:  1.51 (0.43), residues: 172
  sheet: -0.89 (0.31), residues: 252
  loop : -1.74 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0518
  time to fit residues: 3.5122
Evaluate side-chains
  26 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.546 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 2
  average time/residue: 0.0469
  time to fit residues: 0.9326
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0020
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.9996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4066
moved from start:          0.5867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094   5134  Z= 0.466
  Angle     :  1.008   7.912   7138  Z= 0.595
  Chirality :  0.051   0.180    931
  Planarity :  0.008   0.067   1040
  Dihedral  :  8.935  56.432   1013
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 12.37 %
    Favored  : 87.02 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.34 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.23), residues: 994
  helix: -1.03 (0.36), residues: 164
  sheet: -1.19 (0.38), residues: 169
  loop : -2.90 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0453
  time to fit residues: 2.6508
Evaluate side-chains
  23 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.469 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0465
  time to fit residues: 0.9001
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 66 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.9188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4030
moved from start:          0.6270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5134  Z= 0.294
  Angle     :  0.764   8.412   7138  Z= 0.438
  Chirality :  0.047   0.207    931
  Planarity :  0.006   0.064   1040
  Dihedral  :  7.448  52.608   1013
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 12.78 %
    Favored  : 86.82 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.34 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.24), residues: 994
  helix: -0.86 (0.38), residues: 175
  sheet: -1.66 (0.33), residues: 210
  loop : -3.12 (0.22), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0509
  time to fit residues: 3.0674
Evaluate side-chains
  23 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.525 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0460
  time to fit residues: 0.8062
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 95 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4129
moved from start:          0.7830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5134  Z= 0.359
  Angle     :  0.839   7.204   7138  Z= 0.489
  Chirality :  0.048   0.141    931
  Planarity :  0.007   0.070   1040
  Dihedral  :  8.215  58.996   1013
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 17.61 %
    Favored  : 82.09 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.79 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.23), residues: 994
  helix: -1.04 (0.38), residues: 174
  sheet: -1.93 (0.35), residues: 181
  loop : -3.26 (0.21), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0527
  time to fit residues: 3.2661
Evaluate side-chains
  25 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.808 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.0891
  time to fit residues: 1.3091
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 95 optimal weight:    0.3980
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.2788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4151
moved from start:          0.8468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   5134  Z= 0.351
  Angle     :  0.800   7.528   7138  Z= 0.463
  Chirality :  0.046   0.141    931
  Planarity :  0.006   0.067   1040
  Dihedral  :  7.996  59.905   1013
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 16.30 %
    Favored  : 83.40 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.49 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (0.23), residues: 994
  helix: -0.88 (0.40), residues: 162
  sheet: -2.37 (0.34), residues: 182
  loop : -3.23 (0.21), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0525
  time to fit residues: 3.2393
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.565 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.0469
  time to fit residues: 0.9398
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0070
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    2.1604

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4177
moved from start:          0.9522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5134  Z= 0.345
  Angle     :  0.808   8.240   7138  Z= 0.469
  Chirality :  0.046   0.149    931
  Planarity :  0.007   0.067   1040
  Dihedral  :  8.105  59.855   1013
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 19.42 %
    Favored  : 80.38 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.79 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.23), residues: 994
  helix: -0.77 (0.40), residues: 167
  sheet: -2.24 (0.36), residues: 178
  loop : -3.50 (0.20), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0536
  time to fit residues: 3.1267
Evaluate side-chains
  23 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.552 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0484
  time to fit residues: 0.8707
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 53 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0050
   chunk 69 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4065
moved from start:          0.9294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096   5134  Z= 0.235
  Angle     :  0.646  12.757   7138  Z= 0.357
  Chirality :  0.045   0.134    931
  Planarity :  0.005   0.062   1040
  Dihedral  :  6.555  51.440   1013
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.57 %
    Favored  : 88.23 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.09 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.24), residues: 994
  helix: -0.22 (0.41), residues: 171
  sheet: -2.09 (0.37), residues: 187
  loop : -3.32 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 23
  average time/residue: 0.0548
  time to fit residues: 3.2250
Evaluate side-chains
  23 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.559 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0495
  time to fit residues: 0.8589
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0980
   chunk 8 optimal weight:    0.0030
   chunk 60 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.3390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4004
moved from start:          0.9172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   5134  Z= 0.192
  Angle     :  0.557   7.330   7138  Z= 0.304
  Chirality :  0.044   0.138    931
  Planarity :  0.005   0.058   1040
  Dihedral  :  5.342  45.558   1013
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.87 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.09 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.25), residues: 994
  helix:  0.48 (0.44), residues: 168
  sheet: -1.93 (0.35), residues: 215
  loop : -2.99 (0.22), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0536
  time to fit residues: 3.1841
Evaluate side-chains
  24 residues out of total 867 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.588 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.0551
  time to fit residues: 0.9768
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:   20.0000
   chunk 78 optimal weight:    0.0770
   chunk 32 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.0744

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.204405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.189299 restraints weight = 17817.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.189787 restraints weight = 16855.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.191066 restraints weight = 13944.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4577 r_free = 0.4577    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4561 r_free = 0.4561    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      138 |
|-----------------------------------------------------------------------------|
r_final: 0.4561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4404
moved from start:          0.9468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5134  Z= 0.220
  Angle     :  0.595   6.863   7138  Z= 0.333
  Chirality :  0.044   0.130    931
  Planarity :  0.005   0.055   1040
  Dihedral  :  6.011  52.793   1013
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 15.09 %
    Favored  : 84.71 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.09 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.25), residues: 994
  helix:  0.44 (0.43), residues: 168
  sheet: -1.83 (0.37), residues: 196
  loop : -3.03 (0.22), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.000   0.000   TRP A  73 
   PHE   0.000   0.000   PHE A  57 
   TYR   0.000   0.000   TYR A  48 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1225.40 seconds
wall clock time: 22 minutes 28.64 seconds (1348.64 seconds total)