Starting phenix.real_space_refine
on Thu Jul 24 10:54:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2025/8zgo_60085.cif"
  }
  resolution = 2.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Fe      3      7.16       5
     S      26      5.16       5
     C    3953      2.51       5
     N     948      2.21       5
     O    1049      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5980
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 742, 5860
          Classifications: {'peptide': 742}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "A"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 120
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2}
          Classifications: {'undetermined': 4, 'water': 32}
          Link IDs: {None: 35}
  Time building chain proxies: 4.77, per 1000 atoms: 0.80
  Number of scatterers: 5980
  At special positions: 0
  Unit cell: (76.912, 86.108, 101.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      3     26.01
     Ca      1     19.99
     S      26     16.00
     O    1049      8.00
     N     948      7.00
     C    3953      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 883.7 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 2 sheets defined
      76.7% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 3
      No H-bonds generated for 'chain 'A' and resid 1 through 3'
    Processing helix  chain 'A' and resid 4 through 33
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.558A  pdb=" N   THR A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 82 through 105
    Processing helix  chain 'A' and resid 112 through 129
      removed outlier: 3.642A  pdb=" N   VAL A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 161
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 173
    Processing helix  chain 'A' and resid 182 through 200
    Processing helix  chain 'A' and resid 226 through 255
      removed outlier: 4.961A  pdb=" N   SER A 252 " --> pdb=" O   MET A 248 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   PHE A 253 " --> pdb=" O   TRP A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 279
    Processing helix  chain 'A' and resid 280 through 305
      removed outlier: 3.534A  pdb=" N   TYR A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 305 " --> pdb=" O   THR A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.747A  pdb=" N   TRP A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 359
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 366 through 394
    Processing helix  chain 'A' and resid 398 through 400
      No H-bonds generated for 'chain 'A' and resid 398 through 400'
    Processing helix  chain 'A' and resid 401 through 406
    Processing helix  chain 'A' and resid 416 through 436
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 477 through 490
      removed outlier: 3.732A  pdb=" N   VAL A 488 " --> pdb=" O   TRP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 512
    Processing helix  chain 'A' and resid 516 through 536
    Processing helix  chain 'A' and resid 537 through 543
      removed outlier: 3.641A  pdb=" N   LEU A 540 " --> pdb=" O   PRO A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 561
      removed outlier: 3.531A  pdb=" N   ALA A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.580A  pdb=" N   VAL A 568 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 569 " --> pdb=" O   VAL A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 579
      removed outlier: 3.613A  pdb=" N   HIS A 577 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   SER A 579 " --> pdb=" O   TYR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 607
      removed outlier: 3.613A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   PHE A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   VAL A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 614
    Processing helix  chain 'A' and resid 617 through 625
      removed outlier: 4.454A  pdb=" N   TYR A 623 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 658
      removed outlier: 3.934A  pdb=" N   ALA A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   PHE A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 686
      removed outlier: 3.728A  pdb=" N   SER A 686 " --> pdb=" O   MET A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 702 through 708
    Processing helix  chain 'A' and resid 708 through 713
    Processing helix  chain 'A' and resid 714 through 723
    Processing helix  chain 'A' and resid 723 through 746
      removed outlier: 4.230A  pdb=" N   ALA A 727 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 6.706A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72

    398 hydrogen bonds defined for protein.
    1164 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: 1.86

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.17 -     1.53: 5563
        1.53 -     1.89: 576
        1.89 -     2.24: 7
        2.24 -     2.60: 0
        2.60 -     2.96: 1
  Bond restraints: 6147
  Sorted by residual:
  bond pdb=" C   PRO A 267 "
       pdb=" N   SER A 269 "
    ideal  model  delta    sigma   weight residual
    1.332  2.959 -1.626 1.40e-02 5.10e+03 1.35e+04
  bond pdb=" C   VAL A 568 "
       pdb=" N   LEU A 569 "
    ideal  model  delta    sigma   weight residual
    1.335  1.422 -0.088 1.33e-02 5.65e+03 4.35e+01
  bond pdb=" C   PRO A 219 "
       pdb=" O   PRO A 219 "
    ideal  model  delta    sigma   weight residual
    1.237  1.171  0.066 1.32e-02 5.74e+03 2.52e+01
  bond pdb=" C   GLY A  65 "
       pdb=" N   GLY A  66 "
    ideal  model  delta    sigma   weight residual
    1.326  1.406 -0.079 1.64e-02 3.72e+03 2.34e+01
  bond pdb=" C   PRO A 364 "
       pdb=" O   PRO A 364 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.054 1.14e-02 7.69e+03 2.23e+01
  ... (remaining 6142 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 7852
        2.68 -     5.36: 481
        5.36 -     8.05: 61
        8.05 -    10.73: 13
       10.73 -    13.41: 3
  Bond angle restraints: 8410
  Sorted by residual:
  angle pdb=" CA  PRO A 267 "
        pdb=" N   PRO A 267 "
        pdb=" CD  PRO A 267 "
      ideal   model   delta    sigma   weight residual
     112.00   98.59   13.41 1.40e+00 5.10e-01 9.18e+01
  angle pdb=" O   GLN A  62 "
        pdb=" C   GLN A  62 "
        pdb=" N   THR A  63 "
      ideal   model   delta    sigma   weight residual
     122.12  113.08    9.04 1.06e+00 8.90e-01 7.28e+01
  angle pdb=" CA  GLN A  62 "
        pdb=" C   GLN A  62 "
        pdb=" N   THR A  63 "
      ideal   model   delta    sigma   weight residual
     117.30  126.32   -9.02 1.16e+00 7.43e-01 6.04e+01
  angle pdb=" CA  GLY A  65 "
        pdb=" C   GLY A  65 "
        pdb=" O   GLY A  65 "
      ideal   model   delta    sigma   weight residual
     119.03  110.54    8.49 1.14e+00 7.69e-01 5.55e+01
  angle pdb=" C   GLU A 218 "
        pdb=" CA  GLU A 218 "
        pdb=" CB  GLU A 218 "
      ideal   model   delta    sigma   weight residual
     111.02  122.38  -11.36 1.53e+00 4.27e-01 5.52e+01
  ... (remaining 8405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.23: 2999
       18.23 -    36.47: 293
       36.47 -    54.70: 104
       54.70 -    72.94: 11
       72.94 -    91.17: 8
  Dihedral angle restraints: 3415
    sinusoidal: 1287
      harmonic: 2128
  Sorted by residual:
  dihedral pdb=" CA  PRO A 267 "
           pdb=" C   PRO A 267 "
           pdb=" N   SER A 269 "
           pdb=" CA  SER A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.24   49.76     0      5.00e+00 4.00e-02 9.91e+01
  dihedral pdb=" C2C HEM A 801 "
           pdb=" C3C HEM A 801 "
           pdb=" CAC HEM A 801 "
           pdb=" CBC HEM A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -51.48   51.48     2      1.00e+01 1.00e-02 2.94e+01
  dihedral pdb=" C2B HEM A 802 "
           pdb=" C3B HEM A 802 "
           pdb=" CAB HEM A 802 "
           pdb=" CBB HEM A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   44.75  -44.75     2      1.00e+01 1.00e-02 2.38e+01
  ... (remaining 3412 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 720
       0.070 -    0.140: 130
       0.140 -    0.210: 33
       0.210 -    0.280: 14
       0.280 -    0.351: 6
  Chirality restraints: 903
  Sorted by residual:
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CB  VAL A 746 "
            pdb=" CA  VAL A 746 "
            pdb=" CG1 VAL A 746 "
            pdb=" CG2 VAL A 746 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CA  THR A  63 "
            pdb=" N   THR A  63 "
            pdb=" C   THR A  63 "
            pdb=" CB  THR A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 900 not shown)

  Planarity restraints: 1033
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 267 "    0.093 2.00e-02 2.50e+03   1.53e-01 2.34e+02
        pdb=" C   PRO A 267 "   -0.260 2.00e-02 2.50e+03
        pdb=" O   PRO A 267 "    0.125 2.00e-02 2.50e+03
        pdb=" N   SER A 269 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 266 "    0.123 5.00e-02 4.00e+02   1.72e-01 4.74e+01
        pdb=" N   PRO A 267 "   -0.297 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.091 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.083 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 594 "    0.024 2.00e-02 2.50e+03   4.84e-02 2.34e+01
        pdb=" C   LEU A 594 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   LEU A 594 "    0.032 2.00e-02 2.50e+03
        pdb=" N   MET A 595 "    0.028 2.00e-02 2.50e+03
  ... (remaining 1030 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 321
        2.73 -     3.27: 6036
        3.27 -     3.81: 10738
        3.81 -     4.36: 13168
        4.36 -     4.90: 21633
  Nonbonded interactions: 51896
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 542 "
            pdb="FE    FE A 803 "
     model   vdw
     2.182 2.340
  nonbonded pdb=" OG  SER A 338 "
            pdb=" OH  TYR A 386 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" ND1 HIS A 490 "
            pdb="FE    FE A 803 "
     model   vdw
     2.266 2.340
  nonbonded pdb=" O   GLY A 161 "
            pdb=" O   ASN A 177 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   PHE A 663 "
            pdb=" NE2 GLN A 741 "
     model   vdw
     2.316 3.120
  ... (remaining 51891 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.430
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:12.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
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      :  0.023   1.626   6149  Z= 1.601
  Angle     :  1.320  13.411   8410  Z= 0.899
  Chirality :  0.070   0.351    903
  Planarity :  0.012   0.172   1033
  Dihedral  : 16.962  91.173   2059
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.23 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.88 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.47 (0.32), residues: 736
  helix:  0.90 (0.24), residues: 515
  sheet:  None (None), residues: 0
  loop : -0.95 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 342 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.018   0.002   PHE A 639 
 TYR   0.010   0.001   TYR A 375 
 ARG   0.004   0.001   ARG A 724 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16143 (  398)
  hydrogen bonds       : angle       6.16694 ( 1164)
  covalent geometry    : bond        0.02289 ( 6147)
  covalent geometry    : angle       1.32004 ( 8410)
  Misc. bond           : bond        0.06503 (    2)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.7823 (tttt) cc_final: 0.7604 (tmmt)
REVERT: A  321 GLU cc_start: 0.7857 (tt0) cc_final: 0.7585 (tm-30)
REVERT: A  336 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9179 (mp)
REVERT: A  362 LYS cc_start: 0.8000 (mttt) cc_final: 0.7698 (mtmt)
REVERT: A  594 LEU cc_start: 0.6632 (tm) cc_final: 0.6413 (tp)
REVERT: A  662 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (mm-40)
  outliers start: 18
  outliers final: 8
  residues processed: 62
  average time/residue: 1.1719
  time to fit residues: 76.7489
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  662 GLN
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 272 GLN
A 511 ASN
A 625 GLN
A 628 ASN
A 676 ASN
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.087415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.063460 restraints weight = 8505.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 1.65
r_work: 0.2621 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.210   6149  Z= 0.132
  Angle     :  0.606  13.535   8410  Z= 0.291
  Chirality :  0.040   0.121    903
  Planarity :  0.004   0.056   1033
  Dihedral  :  8.650  86.661    832
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.03 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.89 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  1.65 (0.32), residues: 738
  helix:  1.82 (0.24), residues: 517
  sheet:  None (None), residues: 0
  loop : -0.64 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.015   0.001   PHE A 639 
 TYR   0.013   0.001   TYR A 328 
 ARG   0.004   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04982 (  398)
  hydrogen bonds       : angle       4.57042 ( 1164)
  covalent geometry    : bond        0.00299 ( 6147)
  covalent geometry    : angle       0.60597 ( 8410)
  Misc. bond           : bond        0.15397 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  321 GLU cc_start: 0.8140 (tt0) cc_final: 0.7784 (tm-30)
REVERT: A  362 LYS cc_start: 0.8650 (mttt) cc_final: 0.8351 (mtmt)
REVERT: A  498 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7770 (mt-10)
REVERT: A  553 MET cc_start: 0.8728 (mtm) cc_final: 0.8447 (mtm)
  outliers start: 9
  outliers final: 5
  residues processed: 53
  average time/residue: 1.2297
  time to fit residues: 68.9128
Evaluate side-chains
  51 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0020
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.088174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.064403 restraints weight = 8538.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 1.59
r_work: 0.2681 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9027
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.203   6149  Z= 0.136
  Angle     :  0.580  12.798   8410  Z= 0.280
  Chirality :  0.041   0.124    903
  Planarity :  0.004   0.052   1033
  Dihedral  :  7.530  83.215    820
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.05 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  1.90 (0.32), residues: 738
  helix:  2.01 (0.24), residues: 517
  sheet:  None (None), residues: 0
  loop : -0.52 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.019   0.001   PHE A 639 
 TYR   0.012   0.001   TYR A 328 
 ARG   0.002   0.000   ARG A 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04963 (  398)
  hydrogen bonds       : angle       4.47412 ( 1164)
  covalent geometry    : bond        0.00321 ( 6147)
  covalent geometry    : angle       0.57975 ( 8410)
  Misc. bond           : bond        0.14632 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7970 (tt0)
REVERT: A  321 GLU cc_start: 0.8293 (tt0) cc_final: 0.7928 (tm-30)
REVERT: A  368 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7994 (ttm170)
REVERT: A  498 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: A  560 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7926 (m)
  outliers start: 14
  outliers final: 2
  residues processed: 58
  average time/residue: 1.1895
  time to fit residues: 72.9756
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  560 SER
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 62 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.088103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.064341 restraints weight = 8797.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 1.59
r_work: 0.2658 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.179   6149  Z= 0.125
  Angle     :  0.558  11.012   8410  Z= 0.269
  Chirality :  0.040   0.122    903
  Planarity :  0.004   0.051   1033
  Dihedral  :  7.142  81.031    812
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.22 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.00 (0.32), residues: 738
  helix:  2.11 (0.24), residues: 517
  sheet: -2.40 (1.49), residues: 10
  loop : -0.44 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.015   0.001   PHE A 639 
 TYR   0.011   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  398)
  hydrogen bonds       : angle       4.41111 ( 1164)
  covalent geometry    : bond        0.00294 ( 6147)
  covalent geometry    : angle       0.55782 ( 8410)
  Misc. bond           : bond        0.12923 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7861 (tt0)
REVERT: A  368 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7951 (ttm170)
REVERT: A  498 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7995 (mt-10)
  outliers start: 14
  outliers final: 4
  residues processed: 50
  average time/residue: 2.0410
  time to fit residues: 107.3370
Evaluate side-chains
  46 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   chunk 73 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.1980
   chunk 60 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.088118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.064406 restraints weight = 8702.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 1.59
r_work: 0.2660 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2556 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.178   6149  Z= 0.123
  Angle     :  0.547  10.784   8410  Z= 0.264
  Chirality :  0.040   0.121    903
  Planarity :  0.004   0.050   1033
  Dihedral  :  7.083  80.685    812
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.05 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 (0.32), residues: 738
  helix:  2.16 (0.24), residues: 517
  sheet: -2.26 (1.53), residues: 10
  loop : -0.37 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.016   0.001   PHE A 639 
 TYR   0.011   0.001   TYR A 328 
 ARG   0.002   0.000   ARG A 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04596 (  398)
  hydrogen bonds       : angle       4.39686 ( 1164)
  covalent geometry    : bond        0.00290 ( 6147)
  covalent geometry    : angle       0.54678 ( 8410)
  Misc. bond           : bond        0.12878 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A  321 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7739 (tt0)
REVERT: A  368 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7925 (ttm170)
  outliers start: 14
  outliers final: 5
  residues processed: 50
  average time/residue: 1.4027
  time to fit residues: 73.5773
Evaluate side-chains
  48 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 69 optimal weight:    0.4980
   chunk 56 optimal weight:    0.2980
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 21 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.090035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.066600 restraints weight = 8654.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 1.59
r_work: 0.2705 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.141   6149  Z= 0.105
  Angle     :  0.529   9.685   8410  Z= 0.252
  Chirality :  0.039   0.124    903
  Planarity :  0.004   0.050   1033
  Dihedral  :  6.932  80.244    812
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.72 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.16 (0.33), residues: 738
  helix:  2.18 (0.24), residues: 521
  sheet: -2.28 (1.54), residues: 10
  loop : -0.29 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 342 
 HIS   0.007   0.001   HIS A 541 
 PHE   0.015   0.001   PHE A 597 
 TYR   0.008   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  398)
  hydrogen bonds       : angle       4.30764 ( 1164)
  covalent geometry    : bond        0.00236 ( 6147)
  covalent geometry    : angle       0.52853 ( 8410)
  Misc. bond           : bond        0.10183 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7783 (tt0)
REVERT: A  368 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7893 (ttm170)
REVERT: A  434 MET cc_start: 0.9242 (mmm) cc_final: 0.8858 (mmm)
  outliers start: 15
  outliers final: 6
  residues processed: 51
  average time/residue: 1.5569
  time to fit residues: 83.5150
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  712 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 69 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.088609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.064883 restraints weight = 8659.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 1.59
r_work: 0.2669 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2566 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.179   6149  Z= 0.124
  Angle     :  0.558  10.370   8410  Z= 0.267
  Chirality :  0.039   0.121    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.985  80.757    812
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.56 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.16 (0.32), residues: 738
  helix:  2.22 (0.24), residues: 515
  sheet: -2.33 (1.54), residues: 10
  loop : -0.34 (0.44), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.021   0.001   PHE A 597 
 TYR   0.011   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 655 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  398)
  hydrogen bonds       : angle       4.35319 ( 1164)
  covalent geometry    : bond        0.00295 ( 6147)
  covalent geometry    : angle       0.55793 ( 8410)
  Misc. bond           : bond        0.13019 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7785 (tt0)
REVERT: A  336 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8664 (mp)
REVERT: A  368 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7924 (ttm170)
REVERT: A  434 MET cc_start: 0.9244 (mmm) cc_final: 0.8870 (mmm)
  outliers start: 14
  outliers final: 5
  residues processed: 50
  average time/residue: 1.3818
  time to fit residues: 72.9630
Evaluate side-chains
  48 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 39 optimal weight:    0.0980
   chunk 25 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.088165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.064640 restraints weight = 8610.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 1.57
r_work: 0.2663 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8946
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.170   6149  Z= 0.125
  Angle     :  0.553  10.650   8410  Z= 0.265
  Chirality :  0.040   0.123    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.677  80.546    810
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.22 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.15 (0.32), residues: 738
  helix:  2.15 (0.24), residues: 521
  sheet: -2.31 (1.54), residues: 10
  loop : -0.25 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.019   0.001   PHE A 597 
 TYR   0.011   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 655 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 (  398)
  hydrogen bonds       : angle       4.36761 ( 1164)
  covalent geometry    : bond        0.00297 ( 6147)
  covalent geometry    : angle       0.55281 ( 8410)
  Misc. bond           : bond        0.12452 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7795 (tt0)
REVERT: A  336 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8630 (mp)
REVERT: A  368 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7935 (ttm170)
REVERT: A  434 MET cc_start: 0.9249 (mmm) cc_final: 0.8872 (mmm)
REVERT: A  590 LEU cc_start: 0.6293 (pp) cc_final: 0.6071 (pt)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 1.2777
  time to fit residues: 63.1873
Evaluate side-chains
  50 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0570
   chunk 35 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.089191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.065644 restraints weight = 8739.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 1.59
r_work: 0.2685 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8931
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.156   6149  Z= 0.112
  Angle     :  0.542  10.016   8410  Z= 0.259
  Chirality :  0.039   0.116    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.585  79.906    810
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.72 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.15 (0.33), residues: 738
  helix:  2.11 (0.24), residues: 527
  sheet: -2.34 (1.53), residues: 10
  loop : -0.18 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.019   0.001   PHE A 597 
 TYR   0.010   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 707 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  398)
  hydrogen bonds       : angle       4.31783 ( 1164)
  covalent geometry    : bond        0.00261 ( 6147)
  covalent geometry    : angle       0.54171 ( 8410)
  Misc. bond           : bond        0.11310 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7762 (tt0)
REVERT: A  321 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7684 (tt0)
REVERT: A  336 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8618 (mp)
REVERT: A  368 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7917 (ttm170)
REVERT: A  434 MET cc_start: 0.9247 (mmm) cc_final: 0.8866 (mmm)
  outliers start: 11
  outliers final: 4
  residues processed: 47
  average time/residue: 1.5631
  time to fit residues: 77.0817
Evaluate side-chains
  48 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   chunk 60 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0980
   chunk 25 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.089842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.066431 restraints weight = 8701.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 1.59
r_work: 0.2702 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.152   6149  Z= 0.107
  Angle     :  0.534   9.891   8410  Z= 0.254
  Chirality :  0.039   0.144    903
  Planarity :  0.003   0.049   1033
  Dihedral  :  6.522  80.082    810
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.72 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.19 (0.33), residues: 738
  helix:  2.14 (0.24), residues: 527
  sheet: -2.35 (1.55), residues: 10
  loop : -0.15 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 342 
 HIS   0.007   0.001   HIS A 541 
 PHE   0.019   0.001   PHE A 597 
 TYR   0.009   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 707 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  398)
  hydrogen bonds       : angle       4.28624 ( 1164)
  covalent geometry    : bond        0.00246 ( 6147)
  covalent geometry    : angle       0.53420 ( 8410)
  Misc. bond           : bond        0.10965 (    2)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  183 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7736 (tt0)
REVERT: A  321 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7695 (tt0)
REVERT: A  368 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7854 (ttm170)
REVERT: A  434 MET cc_start: 0.9249 (mmm) cc_final: 0.8865 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 47
  average time/residue: 1.4635
  time to fit residues: 72.3802
Evaluate side-chains
  49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  682 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0470
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.089260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.065692 restraints weight = 8746.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 1.59
r_work: 0.2683 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.164   6149  Z= 0.116
  Angle     :  0.548  10.283   8410  Z= 0.262
  Chirality :  0.039   0.117    903
  Planarity :  0.004   0.049   1033
  Dihedral  :  6.532  80.083    810
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.56 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.24 (0.33), residues: 738
  helix:  2.21 (0.24), residues: 521
  sheet: -2.34 (1.55), residues: 10
  loop : -0.15 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 342 
 HIS   0.006   0.001   HIS A 541 
 PHE   0.022   0.001   PHE A 597 
 TYR   0.010   0.001   TYR A 328 
 ARG   0.001   0.000   ARG A 591 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  398)
  hydrogen bonds       : angle       4.30992 ( 1164)
  covalent geometry    : bond        0.00274 ( 6147)
  covalent geometry    : angle       0.54844 ( 8410)
  Misc. bond           : bond        0.11856 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5606.79 seconds
wall clock time: 99 minutes 14.21 seconds (5954.21 seconds total)