Starting phenix.real_space_refine (version: 1.21rc1)
on Fri Apr 21 12:11:14 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/04_2023/7mi3_23838_updated.pdb"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
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=   0.001
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: 8
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      49      5.16       5
     Cl      2      4.86       5
     C    6197      2.51       5
     N    1624      2.21       5
     O    1804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU 2112": "OE1" <-> "OE2"
    Residue "A GLU 2124": "OE1" <-> "OE2"
    Residue "A PHE 2368": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2520": "OE1" <-> "OE2"
    Residue "A ARG 2528": "NH1" <-> "NH2"
    Residue "A ARG 2552": "NH1" <-> "NH2"
    Residue "A TYR 2650": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 2939": "OE1" <-> "OE2"
    Residue "A GLU 2947": "OE1" <-> "OE2"
    Residue "A ARG 2974": "NH1" <-> "NH2"
    Residue "A ARG 2997": "NH1" <-> "NH2"
    Residue "A TYR 3364": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 3365": "NH1" <-> "NH2"
    Residue "A TYR 3389": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 3434": "OE1" <-> "OE2"
    Residue "A ARG 3445": "NH1" <-> "NH2"
    Residue "A PHE 3457": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 3464": "NH1" <-> "NH2"
    Residue "A GLU 3469": "OE1" <-> "OE2"
    Residue "A PHE 3470": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 9682
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1196, 9682
          Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2}
          Classifications: {'peptide': 1192, 'undetermined': 4}
          Link IDs: {'PTRANS': 39, 'TRANS': 1152, None: 4}
            Not linked:
              pdbres="GLU A3523 "
              pdbres="ZG7 A4201 "
            Not linked:
              pdbres="ZG7 A4201 "
              pdbres="ZG7 A4202 "
            Not linked:
              pdbres="ZG7 A4202 "
              pdbres="ATP A4203 "
            Not linked:
              pdbres="ATP A4203 "
              pdbres=" MG A4204 "
          Chain breaks: 1
  Time building chain proxies: 5.42, per 1000 atoms: 0.56
  Number of scatterers: 9682
  At special positions: 0
  Unit cell: (89.096, 137.27, 103.082, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Br      2     34.99
     Cl      2     17.00
     S      49     16.00
     P       3     15.00
     Mg      1     11.99
     O    1804      8.00
     N    1624      7.00
     C    6197      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  - 3.50
        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=0, symmetry=0
  Time building additional restraints: 4.18
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      51.5% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2032 through 2045
    Processing helix  chain 'A' and resid 2051 through 2065
      removed outlier: 3.928A  pdb=" N   LYS A2065 " --> pdb=" O   TYR A2061 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2080 through 2095
    Processing helix  chain 'A' and resid 2106 through 2108
      No H-bonds generated for 'chain 'A' and resid 2106 through 2108'
    Processing helix  chain 'A' and resid 2111 through 2114
      No H-bonds generated for 'chain 'A' and resid 2111 through 2114'
    Processing helix  chain 'A' and resid 2129 through 2139
    Processing helix  chain 'A' and resid 2160 through 2170
      removed outlier: 3.564A  pdb=" N   MET A2166 " --> pdb=" O   TYR A2162 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER A2168 " --> pdb=" O   GLU A2164 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL A2169 " --> pdb=" O   ALA A2165 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU A2170 " --> pdb=" O   MET A2166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2204 through 2209
      removed outlier: 3.689A  pdb=" N   ARG A2209 " --> pdb=" O   ALA A2205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2222 through 2240
      removed outlier: 3.803A  pdb=" N   ALA A2236 " --> pdb=" O   LYS A2232 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ASN A2239 " --> pdb=" O   GLU A2235 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LYS A2240 " --> pdb=" O   ALA A2236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2243 through 2257
      removed outlier: 4.074A  pdb=" N   LYS A2248 " --> pdb=" O   PHE A2244 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A2255 " --> pdb=" O   ASP A2251 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   SER A2256 " --> pdb=" O   LEU A2252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2260 through 2267
    Processing helix  chain 'A' and resid 2280 through 2282
      No H-bonds generated for 'chain 'A' and resid 2280 through 2282'
    Processing helix  chain 'A' and resid 2284 through 2304
      removed outlier: 3.805A  pdb=" N   TYR A2298 " --> pdb=" O   LEU A2294 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ARG A2299 " --> pdb=" O   ILE A2295 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   GLN A2300 " --> pdb=" O   SER A2296 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   TRP A2301 " --> pdb=" O   SER A2297 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLN A2303 " --> pdb=" O   ARG A2299 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ASN A2304 " --> pdb=" O   GLN A2300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2307 through 2327
    Processing helix  chain 'A' and resid 2333 through 2345
      removed outlier: 3.857A  pdb=" N   GLN A2340 " --> pdb=" O   ARG A2336 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR A2341 " --> pdb=" O   ALA A2337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2386
    Processing helix  chain 'A' and resid 2395 through 2409
    Processing helix  chain 'A' and resid 2424 through 2434
      removed outlier: 3.842A  pdb=" N   MET A2428 " --> pdb=" O   LYS A2424 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASN A2434 " --> pdb=" O   ASN A2430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2451 through 2461
      removed outlier: 4.234A  pdb=" N   ARG A2460 " --> pdb=" O   SER A2456 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   HIS A2461 " --> pdb=" O   ALA A2457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2501 through 2512
    Processing helix  chain 'A' and resid 2548 through 2553
      removed outlier: 4.521A  pdb=" N   HIS A2553 " --> pdb=" O   ARG A2549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2565 through 2581
      removed outlier: 4.569A  pdb=" N   LEU A2581 " --> pdb=" O   ALA A2577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2583 through 2606
      removed outlier: 4.799A  pdb=" N   SER A2587 " --> pdb=" O   GLU A2584 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLU A2590 " --> pdb=" O   SER A2587 " (cutoff:3.500A)
      Proline residue:  A2591  - end of helix
    Processing helix  chain 'A' and resid 2619 through 2634
      removed outlier: 3.525A  pdb=" N   ARG A2624 " --> pdb=" O   GLU A2621 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A2629 " --> pdb=" O   VAL A2626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2641 through 2659
      removed outlier: 4.906A  pdb=" N   ASP A2658 " --> pdb=" O   ARG A2654 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   ARG A2659 " --> pdb=" O   ILE A2655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2663 through 2680
    Processing helix  chain 'A' and resid 2709 through 2726
    Processing helix  chain 'A' and resid 2736 through 2750
    Processing helix  chain 'A' and resid 2766 through 2777
      removed outlier: 3.526A  pdb=" N   ARG A2771 " --> pdb=" O   THR A2767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2792 through 2808
    Processing helix  chain 'A' and resid 2819 through 2821
      No H-bonds generated for 'chain 'A' and resid 2819 through 2821'
    Processing helix  chain 'A' and resid 2825 through 2836
    Processing helix  chain 'A' and resid 2841 through 2844
    Processing helix  chain 'A' and resid 2846 through 2863
      removed outlier: 3.557A  pdb=" N   LYS A2851 " --> pdb=" O   GLU A2848 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR A2860 " --> pdb=" O   ARG A2857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2870 through 2884
    Processing helix  chain 'A' and resid 2897 through 2904
    Processing helix  chain 'A' and resid 2906 through 2909
      No H-bonds generated for 'chain 'A' and resid 2906 through 2909'
    Processing helix  chain 'A' and resid 2922 through 2935
      removed outlier: 3.994A  pdb=" N   VAL A2935 " --> pdb=" O   ASN A2931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2942 through 2944
      No H-bonds generated for 'chain 'A' and resid 2942 through 2944'
    Processing helix  chain 'A' and resid 2961 through 2979
    Processing helix  chain 'A' and resid 2990 through 3010
      removed outlier: 3.600A  pdb=" N   VAL A3000 " --> pdb=" O   LEU A2996 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A3001 " --> pdb=" O   ARG A2997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3317 through 3336
      removed outlier: 3.789A  pdb=" N   ILE A3321 " --> pdb=" O   GLN A3318 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   TYR A3333 " --> pdb=" O   TYR A3330 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   PHE A3334 " --> pdb=" O   GLU A3331 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   GLY A3335 " --> pdb=" O   THR A3332 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   HIS A3336 " --> pdb=" O   TYR A3333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3339 through 3355
      removed outlier: 3.746A  pdb=" N   LEU A3352 " --> pdb=" O   ILE A3348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3366 through 3370
    Processing helix  chain 'A' and resid 3373 through 3381
      removed outlier: 4.105A  pdb=" N   LEU A3380 " --> pdb=" O   LYS A3376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3388 through 3399
    Processing helix  chain 'A' and resid 3414 through 3425
      removed outlier: 4.237A  pdb=" N   SER A3419 " --> pdb=" O   ILE A3415 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ASN A3424 " --> pdb=" O   ASN A3420 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LYS A3425 " --> pdb=" O   TYR A3421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3436 through 3446
    Processing helix  chain 'A' and resid 3460 through 3466
      removed outlier: 4.394A  pdb=" N   ARG A3464 " --> pdb=" O   ILE A3461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3507 through 3510
      No H-bonds generated for 'chain 'A' and resid 3507 through 3510'
    Processing sheet with id=  A, first strand: chain 'A' and resid 2211 through 2215
      removed outlier: 8.827A  pdb=" N   LEU A2070 " --> pdb=" O   PHE A2190 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ILE A2192 " --> pdb=" O   LEU A2070 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   LEU A2072 " --> pdb=" O   ILE A2192 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   PHE A2194 " --> pdb=" O   LEU A2072 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   GLY A2074 " --> pdb=" O   PHE A2194 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   THR A2196 " --> pdb=" O   GLY A2074 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ARG A2191 " --> pdb=" O   SER A2148 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ILE A2150 " --> pdb=" O   ARG A2191 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU A2193 " --> pdb=" O   ILE A2150 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A2152 " --> pdb=" O   LEU A2193 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   GLU A2195 " --> pdb=" O   VAL A2152 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ALA A2098 " --> pdb=" O   ARG A2149 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   TRP A2151 " --> pdb=" O   ALA A2098 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A2100 " --> pdb=" O   TRP A2151 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL A2153 " --> pdb=" O   VAL A2100 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   TYR A2102 " --> pdb=" O   VAL A2153 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 2175 through 2177
    Processing sheet with id=  C, first strand: chain 'A' and resid 2358 through 2361
      removed outlier: 3.589A  pdb=" N   THR A2358 " --> pdb=" O   PHE A2371 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 2554 through 2559
      removed outlier: 6.762A  pdb=" N   GLY A2413 " --> pdb=" O   ALA A2555 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   LEU A2557 " --> pdb=" O   GLY A2413 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE A2415 " --> pdb=" O   LEU A2557 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU A2559 " --> pdb=" O   ILE A2415 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   CYS A2417 " --> pdb=" O   LEU A2559 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A2414 " --> pdb=" O   ILE A2531 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU A2482 " --> pdb=" O   HIS A2530 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A2532 " --> pdb=" O   LEU A2482 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU A2484 " --> pdb=" O   VAL A2532 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ALA A2534 " --> pdb=" O   LEU A2484 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   CYS A2486 " --> pdb=" O   ALA A2534 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 2465 through 2467
    Processing sheet with id=  F, first strand: chain 'A' and resid 2780 through 2783
      removed outlier: 6.863A  pdb=" N   MET A2756 " --> pdb=" O   PHE A2889 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ILE A2891 " --> pdb=" O   MET A2756 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A2758 " --> pdb=" O   ILE A2891 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 3514 through 3517
      removed outlier: 7.538A  pdb=" N   LEU A3494 " --> pdb=" O   PRO A3405 " (cutoff:3.500A)
      removed outlier: 8.458A  pdb=" N   LEU A3407 " --> pdb=" O   LEU A3494 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE A3496 " --> pdb=" O   LEU A3407 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 3478 through 3481
      removed outlier: 3.591A  pdb=" N   HIS A3484 " --> pdb=" O   ILE A3481 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1110 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: 3.55

  Time building geometry restraints manager: 4.47 seconds

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

  Histogram of bond lengths:
        1.13 -     1.29: 1587
        1.29 -     1.46: 3126
        1.46 -     1.62: 5093
        1.62 -     1.78: 18
        1.78 -     1.94: 65
  Bond restraints: 9889
  Sorted by residual:
  bond pdb=" C14 ZG7 A4202 "
       pdb=" N15 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.328  1.531 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C14 ZG7 A4201 "
       pdb=" N15 ZG7 A4201 "
    ideal  model  delta    sigma   weight residual
    1.328  1.520 -0.192 2.00e-02 2.50e+03 9.21e+01
  bond pdb=" C5  ATP A4203 "
       pdb=" C6  ATP A4203 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.87e+01
  bond pdb=" C26 ZG7 A4202 "
       pdb=" O27 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.305  1.166  0.139 2.00e-02 2.50e+03 4.80e+01
  bond pdb=" C16 ZG7 A4202 "
       pdb=" N15 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.312  1.450 -0.138 2.00e-02 2.50e+03 4.77e+01
  ... (remaining 9884 not shown)

  Histogram of bond angle deviations from ideal:
       59.63 -    83.58: 6
       83.58 -   107.53: 456
      107.53 -   131.48: 12908
      131.48 -   155.43: 31
      155.43 -   179.38: 2
  Bond angle restraints: 13403
  Sorted by residual:
  angle pdb=" PA  ATP A4203 "
        pdb=" O3A ATP A4203 "
        pdb=" PB  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     136.83  121.50   15.33 1.00e+00 1.00e+00 2.35e+02
  angle pdb=" PB  ATP A4203 "
        pdb=" O3B ATP A4203 "
        pdb=" PG  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     139.87  128.63   11.24 1.00e+00 1.00e+00 1.26e+02
  angle pdb=" C5  ATP A4203 "
        pdb=" C4  ATP A4203 "
        pdb=" N3  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     126.80  118.41    8.39 1.00e+00 1.00e+00 7.04e+01
  angle pdb=" N   TYR A2115 "
        pdb=" CA  TYR A2115 "
        pdb=" C   TYR A2115 "
      ideal   model   delta    sigma   weight residual
     110.17   99.76   10.41 1.51e+00 4.39e-01 4.75e+01
  angle pdb=" N3  ATP A4203 "
        pdb=" C4  ATP A4203 "
        pdb=" N9  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     127.04  134.67   -7.63 1.15e+00 7.59e-01 4.41e+01
  ... (remaining 13398 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5529
       17.88 -    35.76: 302
       35.76 -    53.64: 45
       53.64 -    71.53: 24
       71.53 -    89.41: 13
  Dihedral angle restraints: 5913
    sinusoidal: 2411
      harmonic: 3502
  Sorted by residual:
  dihedral pdb=" CA  ASP A2105 "
           pdb=" C   ASP A2105 "
           pdb=" N   THR A2106 "
           pdb=" CA  THR A2106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.51  -26.49     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  GLN A2639 "
           pdb=" C   GLN A2639 "
           pdb=" N   THR A2640 "
           pdb=" CA  THR A2640 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.29   25.71     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  GLU A2810 "
           pdb=" C   GLU A2810 "
           pdb=" N   SER A2811 "
           pdb=" CA  SER A2811 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 5910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1157
       0.085 -    0.169: 315
       0.169 -    0.254: 37
       0.254 -    0.338: 7
       0.338 -    0.423: 4
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CB  ILE A2226 "
            pdb=" CA  ILE A2226 "
            pdb=" CG1 ILE A2226 "
            pdb=" CG2 ILE A2226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CB  ILE A2141 "
            pdb=" CA  ILE A2141 "
            pdb=" CG1 ILE A2141 "
            pdb=" CG2 ILE A2141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.00   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  LEU A2366 "
            pdb=" N   LEU A2366 "
            pdb=" C   LEU A2366 "
            pdb=" CB  LEU A2366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.09e+00
  ... (remaining 1517 not shown)

  Planarity restraints: 1686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 ZG7 A4202 "   -0.014 2.00e-02 2.50e+03   2.73e-02 2.61e+01
        pdb=" C11 ZG7 A4202 "    0.067 2.00e-02 2.50e+03
        pdb=" C14 ZG7 A4202 "   -0.009 2.00e-02 2.50e+03
        pdb=" C16 ZG7 A4202 "   -0.015 2.00e-02 2.50e+03
        pdb=" C17 ZG7 A4202 "   -0.012 2.00e-02 2.50e+03
        pdb=" C26 ZG7 A4202 "    0.002 2.00e-02 2.50e+03
        pdb=" C28 ZG7 A4202 "   -0.018 2.00e-02 2.50e+03
        pdb=" C29 ZG7 A4202 "    0.003 2.00e-02 2.50e+03
        pdb=" N12 ZG7 A4202 "   -0.005 2.00e-02 2.50e+03
        pdb=" N13 ZG7 A4202 "   -0.029 2.00e-02 2.50e+03
        pdb=" N15 ZG7 A4202 "   -0.009 2.00e-02 2.50e+03
        pdb=" N30 ZG7 A4202 "    0.010 2.00e-02 2.50e+03
        pdb=" O18 ZG7 A4202 "    0.056 2.00e-02 2.50e+03
        pdb=" O27 ZG7 A4202 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A2728 "   -0.018 2.00e-02 2.50e+03   3.57e-02 1.28e+01
        pdb=" C   LEU A2728 "    0.062 2.00e-02 2.50e+03
        pdb=" O   LEU A2728 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A2729 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 ZG7 A4202 "   -0.003 2.00e-02 2.50e+03   2.42e-02 1.17e+01
        pdb=" C03 ZG7 A4202 "   -0.003 2.00e-02 2.50e+03
        pdb=" C04 ZG7 A4202 "   -0.006 2.00e-02 2.50e+03
        pdb=" C05 ZG7 A4202 "    0.059 2.00e-02 2.50e+03
        pdb=" C06 ZG7 A4202 "   -0.002 2.00e-02 2.50e+03
        pdb=" C07 ZG7 A4202 "   -0.005 2.00e-02 2.50e+03
        pdb=" C08 ZG7 A4202 "   -0.034 2.00e-02 2.50e+03
        pdb="CL01 ZG7 A4202 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1683 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 68
        2.56 -     3.15: 8279
        3.15 -     3.73: 14789
        3.73 -     4.32: 20691
        4.32 -     4.90: 33976
  Nonbonded interactions: 77803
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A4203 "
            pdb="MG    MG A4204 "
     model   vdw
     1.978 2.170
  nonbonded pdb=" OG1 THR A2081 "
            pdb="MG    MG A4204 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" O1B ATP A4203 "
            pdb="MG    MG A4204 "
     model   vdw
     2.038 2.170
  nonbonded pdb=" OD1 ASN A2832 "
            pdb=" OG  SER A2905 "
     model   vdw
     2.263 2.440
  nonbonded pdb=" NH1 ARG A2763 "
            pdb=" O   SER A3511 "
     model   vdw
     2.298 2.520
  ... (remaining 77798 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=0.50 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:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          11.490
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     28.490
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.010
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
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      :  0.012   0.203   9889  Z= 0.793
  Angle     :  1.474  19.050  13403  Z= 0.824
  Chirality :  0.078   0.423   1520
  Planarity :  0.008   0.054   1686
  Dihedral  : 12.839  89.407   3641
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.82 %
    Favored  : 92.85 %
  Rotamer Outliers :  1.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.22), residues: 1188
  helix: -0.54 (0.19), residues: 584
  sheet: -1.71 (0.43), residues: 125
  loop : -1.75 (0.26), residues: 479

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 7
  residues processed: 239
  average time/residue: 0.2706
  time to fit residues: 85.3130
Evaluate side-chains
  109 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 1.289 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.1339
  time to fit residues: 3.1629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A2300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2363 ASN
A2481 ASN
A2569 GLN
A2854 ASN
** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3471 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9889  Z= 0.182
  Angle     :  0.666   8.549  13403  Z= 0.344
  Chirality :  0.044   0.199   1520
  Planarity :  0.004   0.042   1686
  Dihedral  :  6.885  89.366   1300
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.78 %
    Favored  : 97.05 %
  Rotamer Outliers :  2.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.24), residues: 1188
  helix:  0.71 (0.21), residues: 607
  sheet: -1.07 (0.43), residues: 137
  loop : -1.15 (0.29), residues: 444

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 15
  residues processed: 153
  average time/residue: 0.2395
  time to fit residues: 50.8497
Evaluate side-chains
  116 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.160 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 15
  outliers final: 1
  residues processed: 15
  average time/residue: 0.1377
  time to fit residues: 4.8615
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   chunk 116 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A2274 HIS
** A2300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2500 GLN
A2598 HIS
A3471 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9889  Z= 0.213
  Angle     :  0.607   8.321  13403  Z= 0.312
  Chirality :  0.042   0.146   1520
  Planarity :  0.004   0.043   1686
  Dihedral  :  6.641  89.409   1300
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.46 %
  Rotamer Outliers :  2.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1188
  helix:  1.04 (0.21), residues: 600
  sheet: -0.91 (0.43), residues: 143
  loop : -0.91 (0.29), residues: 445

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2445
  time to fit residues: 44.6236
Evaluate side-chains
  110 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.272 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 11
  average time/residue: 0.1284
  time to fit residues: 4.0744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 81 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 102 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A2300 GLN
** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3471 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9889  Z= 0.174
  Angle     :  0.577   8.796  13403  Z= 0.292
  Chirality :  0.042   0.160   1520
  Planarity :  0.004   0.040   1686
  Dihedral  :  6.432  87.263   1300
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer Outliers :  1.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1188
  helix:  1.11 (0.22), residues: 592
  sheet: -0.65 (0.43), residues: 144
  loop : -0.70 (0.29), residues: 452

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 7
  residues processed: 120
  average time/residue: 0.2480
  time to fit residues: 41.5633
Evaluate side-chains
  96 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.282 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.1418
  time to fit residues: 3.2289
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A3471 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.078   9889  Z= 0.481
  Angle     :  0.726   8.617  13403  Z= 0.373
  Chirality :  0.046   0.177   1520
  Planarity :  0.005   0.059   1686
  Dihedral  :  6.776  89.950   1300
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.38 %
    Favored  : 95.54 %
  Rotamer Outliers :  2.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.24), residues: 1188
  helix:  0.95 (0.21), residues: 591
  sheet: -0.50 (0.43), residues: 140
  loop : -0.90 (0.28), residues: 457

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 11
  residues processed: 110
  average time/residue: 0.2397
  time to fit residues: 37.5243
Evaluate side-chains
  95 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.213 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 11
  average time/residue: 0.1245
  time to fit residues: 3.8776
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 115 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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: 0.8667
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9889  Z= 0.258
  Angle     :  0.612   8.855  13403  Z= 0.307
  Chirality :  0.042   0.177   1520
  Planarity :  0.004   0.057   1686
  Dihedral  :  6.543  88.897   1300
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.12 %
    Favored  : 95.79 %
  Rotamer Outliers :  1.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1188
  helix:  1.16 (0.22), residues: 590
  sheet: -0.36 (0.42), residues: 144
  loop : -0.78 (0.29), residues: 454

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 1.277 
Fit side-chains
  outliers start: 21
  outliers final: 7
  residues processed: 116
  average time/residue: 0.2409
  time to fit residues: 39.5359
Evaluate side-chains
  96 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.224 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.1475
  time to fit residues: 3.2746
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0050
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.9200

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9889  Z= 0.200
  Angle     :  0.592   9.736  13403  Z= 0.296
  Chirality :  0.042   0.172   1520
  Planarity :  0.004   0.056   1686
  Dihedral  :  6.391  88.188   1300
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer Outliers :  1.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1188
  helix:  1.33 (0.22), residues: 585
  sheet: -0.15 (0.41), residues: 154
  loop : -0.60 (0.29), residues: 449

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 3
  residues processed: 112
  average time/residue: 0.2431
  time to fit residues: 38.7548
Evaluate side-chains
  94 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 1.197 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 3
  average time/residue: 0.1920
  time to fit residues: 2.4822
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   chunk 104 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3497 HIS
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9889  Z= 0.191
  Angle     :  0.598  14.364  13403  Z= 0.293
  Chirality :  0.041   0.164   1520
  Planarity :  0.004   0.057   1686
  Dihedral  :  6.287  87.738   1300
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer Outliers :  0.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1188
  helix:  1.42 (0.22), residues: 577
  sheet: -0.11 (0.41), residues: 157
  loop : -0.55 (0.29), residues: 454

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 107
  average time/residue: 0.2515
  time to fit residues: 37.8683
Evaluate side-chains
  95 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.349 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 3
  average time/residue: 0.3141
  time to fit residues: 2.9474
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9889  Z= 0.196
  Angle     :  0.597  16.544  13403  Z= 0.294
  Chirality :  0.041   0.165   1520
  Planarity :  0.004   0.057   1686
  Dihedral  :  6.260  87.871   1300
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer Outliers :  0.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.25), residues: 1188
  helix:  1.42 (0.22), residues: 578
  sheet: -0.03 (0.42), residues: 157
  loop : -0.58 (0.29), residues: 453

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 103
  average time/residue: 0.2228
  time to fit residues: 33.4486
Evaluate side-chains
  95 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 1.277 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 4
  average time/residue: 0.1915
  time to fit residues: 2.7159
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A2735 HIS
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9889  Z= 0.224
  Angle     :  0.614  16.214  13403  Z= 0.303
  Chirality :  0.042   0.165   1520
  Planarity :  0.004   0.058   1686
  Dihedral  :  6.295  88.223   1300
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer Outliers :  0.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1188
  helix:  1.39 (0.22), residues: 578
  sheet: -0.01 (0.42), residues: 157
  loop : -0.64 (0.29), residues: 453

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 95
  average time/residue: 0.2205
  time to fit residues: 30.9260
Evaluate side-chains
  89 residues out of total 1084 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 1.125 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.5118
  time to fit residues: 2.2125
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 94 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0030
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.4592

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.071852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.056018 restraints weight = 30841.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.058259 restraints weight = 15192.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.059846 restraints weight = 9624.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9889  Z= 0.170
  Angle     :  0.595  16.461  13403  Z= 0.292
  Chirality :  0.042   0.214   1520
  Planarity :  0.004   0.058   1686
  Dihedral  :  6.224  87.889   1300
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer Outliers :  0.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1188
  helix:  1.43 (0.23), residues: 578
  sheet:  0.10 (0.42), residues: 157
  loop : -0.60 (0.29), residues: 453

===============================================================================
Job complete
usr+sys time: 2360.66 seconds
wall clock time: 43 minutes 36.11 seconds (2616.11 seconds total)