Starting phenix.real_space_refine
on Wed Sep 17 03:00:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kom_62478/09_2025/9kom_62478.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1485      2.51       5
     N     377      2.21       5
     O     396      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2268
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2268
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 13, 'TRANS': 277}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 50
  Time building chain proxies: 1.01, per 1000 atoms: 0.45
  Number of scatterers: 2268
  At special positions: 0
  Unit cell: (60.48, 50.4, 119.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     396      8.00
     N     377      7.00
     C    1485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 242 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 113.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  568

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 1 sheets defined
      69.8% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 61
      Proline residue:  A  46  - end of helix
      removed outlier: 4.291A  pdb=" N   GLN A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 4.443A  pdb=" N   LYS A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
      removed outlier: 3.545A  pdb=" N   ALA A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 132 through 159
      removed outlier: 3.825A  pdb=" N   ARG A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 201
      removed outlier: 3.991A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 231
      removed outlier: 3.809A  pdb=" N   ASN A 213 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 235
      removed outlier: 3.592A  pdb=" N   PHE A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 235'
    Processing helix  chain 'A' and resid 265 through 294
      removed outlier: 3.967A  pdb=" N   VAL A 284 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
      removed outlier: 4.574A  pdb=" N   LEU A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
      removed outlier: 3.634A  pdb=" N   LYS A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 368 through 374
      removed outlier: 4.295A  pdb=" N   GLY A 374 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66

    137 hydrogen bonds defined for protein.
    408 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: 0.35

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 698
        1.34 -     1.46: 559
        1.46 -     1.58: 1048
        1.58 -     1.70: 0
        1.70 -     1.81: 13
  Bond restraints: 2318
  Sorted by residual:
  bond pdb=" CB  GLU A 193 "
       pdb=" CG  GLU A 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CB  GLU A 252 "
       pdb=" CG  GLU A 252 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CB  TYR A 151 "
       pdb=" CG  TYR A 151 "
    ideal  model  delta    sigma   weight residual
    1.512  1.535 -0.023 2.20e-02 2.07e+03 1.05e+00
  bond pdb=" CB  ASP A 148 "
       pdb=" CG  ASP A 148 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.68e-01
  bond pdb=" C   TRP A 105 "
       pdb=" N   PRO A 106 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.012 1.28e-02 6.10e+03 8.41e-01
  ... (remaining 2313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3063
        1.82 -     3.65: 58
        3.65 -     5.47: 14
        5.47 -     7.30: 14
        7.30 -     9.12: 2
  Bond angle restraints: 3151
  Sorted by residual:
  angle pdb=" CA  GLU A 193 "
        pdb=" CB  GLU A 193 "
        pdb=" CG  GLU A 193 "
      ideal   model   delta    sigma   weight residual
     114.10  121.32   -7.22 2.00e+00 2.50e-01 1.30e+01
  angle pdb=" CA  TYR A 151 "
        pdb=" CB  TYR A 151 "
        pdb=" CG  TYR A 151 "
      ideal   model   delta    sigma   weight residual
     113.90  120.40   -6.50 1.80e+00 3.09e-01 1.30e+01
  angle pdb=" CB  MET A 121 "
        pdb=" CG  MET A 121 "
        pdb=" SD  MET A 121 "
      ideal   model   delta    sigma   weight residual
     112.70  121.82   -9.12 3.00e+00 1.11e-01 9.25e+00
  angle pdb=" CA  GLU A 252 "
        pdb=" CB  GLU A 252 "
        pdb=" CG  GLU A 252 "
      ideal   model   delta    sigma   weight residual
     114.10  120.06   -5.96 2.00e+00 2.50e-01 8.88e+00
  angle pdb=" CB  GLU A 252 "
        pdb=" CG  GLU A 252 "
        pdb=" CD  GLU A 252 "
      ideal   model   delta    sigma   weight residual
     112.60  117.60   -5.00 1.70e+00 3.46e-01 8.65e+00
  ... (remaining 3146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 1135
       16.00 -    32.01: 185
       32.01 -    48.01: 60
       48.01 -    64.01: 10
       64.01 -    80.02: 3
  Dihedral angle restraints: 1393
    sinusoidal: 528
      harmonic: 865
  Sorted by residual:
  dihedral pdb=" CA  GLU A 252 "
           pdb=" C   GLU A 252 "
           pdb=" N   THR A 253 "
           pdb=" CA  THR A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  dihedral pdb=" N   ASN A 152 "
           pdb=" CA  ASN A 152 "
           pdb=" CB  ASN A 152 "
           pdb=" CG  ASN A 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.98   56.98     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CA  HIS A 203 "
           pdb=" C   HIS A 203 "
           pdb=" N   SER A 204 "
           pdb=" CA  SER A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.71  -15.29     0      5.00e+00 4.00e-02 9.35e+00
  ... (remaining 1390 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 233
       0.030 -    0.060: 89
       0.060 -    0.090: 40
       0.090 -    0.120: 15
       0.120 -    0.150: 4
  Chirality restraints: 381
  Sorted by residual:
  chirality pdb=" CA  SER A  45 "
            pdb=" N   SER A  45 "
            pdb=" C   SER A  45 "
            pdb=" CB  SER A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.63e-01
  chirality pdb=" CA  TRP A 105 "
            pdb=" N   TRP A 105 "
            pdb=" C   TRP A 105 "
            pdb=" CB  TRP A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 378 not shown)

  Planarity restraints: 383
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 193 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" CD  GLU A 193 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 193 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 193 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 252 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" CD  GLU A 252 "   -0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 252 "    0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 252 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 105 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 106 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 106 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 106 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 380 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 509
        2.78 -     3.31: 2115
        3.31 -     3.84: 3654
        3.84 -     4.37: 3531
        4.37 -     4.90: 6478
  Nonbonded interactions: 16287
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 224 "
            pdb=" OG1 THR A 281 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PRO A 322 "
            pdb=" ND2 ASN A 327 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" N   GLU A 238 "
            pdb=" OE1 GLU A 238 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OD1 ASP A  35 "
            pdb=" ND2 ASN A 290 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   ARG A 156 "
            pdb=" NE2 GLN A 159 "
     model   vdw
     2.334 3.120
  ... (remaining 16282 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:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.180
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6096
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2320  Z= 0.165
  Angle     :  0.786   9.122   3155  Z= 0.400
  Chirality :  0.042   0.150    381
  Planarity :  0.004   0.039    383
  Dihedral  : 17.934  80.018    819
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 41.13 %
    Favored  : 58.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.52), residues: 281
  helix:  1.05 (0.39), residues: 189
  sheet: -1.11 (1.37), residues: 18
  loop : -1.55 (0.72), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 316 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.018   0.002   PHE A 189 
 TRP   0.011   0.001   TRP A 297 
 HIS   0.001   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2318)
  covalent geometry    : angle       0.78645 ( 3151)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       0.31387 (    4)
  hydrogen bonds       : bond        0.17102 (  137)
  hydrogen bonds       : angle       5.48582 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6607 (ttp-110)
REVERT: A  129 GLN cc_start: 0.6987 (tp40) cc_final: 0.6477 (tt0)
REVERT: A  194 ARG cc_start: 0.6344 (mtm-85) cc_final: 0.5518 (tmt170)
REVERT: A  201 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6291 (ttm110)
REVERT: A  237 GLN cc_start: 0.7236 (tp40) cc_final: 0.6987 (tp40)
REVERT: A  239 GLU cc_start: 0.8092 (pt0) cc_final: 0.7826 (pt0)
REVERT: A  257 ASN cc_start: 0.7784 (t0) cc_final: 0.7263 (t0)
REVERT: A  262 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6202 (ttm-80)
REVERT: A  331 LEU cc_start: 0.4607 (mt) cc_final: 0.4329 (mp)
REVERT: A  334 ARG cc_start: 0.6149 (tmm-80) cc_final: 0.5511 (tmm160)
  outliers start: 2
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1142
  time to fit residues: 5.0635
Evaluate side-chains
  28 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 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 = 0.3901 r_free = 0.3901 target = 0.168541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124102 restraints weight = 2348.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.65
r_work: 0.3155 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2320  Z= 0.135
  Angle     :  0.607   7.374   3155  Z= 0.297
  Chirality :  0.038   0.128    381
  Planarity :  0.004   0.036    383
  Dihedral  :  3.780  14.830    311
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 38.31 %
    Favored  : 57.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.52), residues: 281
  helix:  1.37 (0.39), residues: 192
  sheet: -1.16 (1.33), residues: 18
  loop : -1.74 (0.71), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.012   0.001   TYR A 280 
 PHE   0.009   0.001   PHE A 269 
 TRP   0.007   0.001   TRP A 297 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 2318)
  covalent geometry    : angle       0.60730 ( 3151)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       0.44375 (    4)
  hydrogen bonds       : bond        0.04480 (  137)
  hydrogen bonds       : angle       4.18292 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7256 (ttp-110)
REVERT: A  200 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6526 (tt0)
REVERT: A  201 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.6841 (ttm110)
REVERT: A  262 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8113 (ttm-80)
REVERT: A  334 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.6967 (tmm160)
  outliers start: 10
  outliers final: 6
  residues processed: 36
  average time/residue: 0.0997
  time to fit residues: 4.0658
Evaluate side-chains
  29 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 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 = 0.3892 r_free = 0.3892 target = 0.168173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.122658 restraints weight = 2431.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.70
r_work: 0.3159 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   2320  Z= 0.111
  Angle     :  0.540   6.658   3155  Z= 0.261
  Chirality :  0.037   0.122    381
  Planarity :  0.005   0.059    383
  Dihedral  :  3.478  14.293    311
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 37.10 %
    Favored  : 58.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.52), residues: 281
  helix:  1.69 (0.39), residues: 192
  sheet: -1.18 (1.30), residues: 18
  loop : -1.69 (0.70), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 153 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.009   0.001   PHE A  58 
 TRP   0.007   0.001   TRP A 105 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2318)
  covalent geometry    : angle       0.54017 ( 3151)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.34946 (    4)
  hydrogen bonds       : bond        0.03743 (  137)
  hydrogen bonds       : angle       3.87588 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7020 (ttm170)
REVERT: A  108 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8143 (tttm)
REVERT: A  200 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6693 (tt0)
REVERT: A  201 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.6914 (ttm110)
REVERT: A  233 ASP cc_start: 0.7920 (m-30) cc_final: 0.7668 (m-30)
REVERT: A  262 ARG cc_start: 0.8471 (ttt90) cc_final: 0.8092 (ttm-80)
REVERT: A  331 LEU cc_start: 0.6837 (mt) cc_final: 0.6636 (mp)
REVERT: A  334 ARG cc_start: 0.7548 (tmm-80) cc_final: 0.6980 (tmm160)
  outliers start: 12
  outliers final: 9
  residues processed: 37
  average time/residue: 0.1016
  time to fit residues: 4.2159
Evaluate side-chains
  34 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 25
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  318 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 4 optimal weight:    0.0570
   chunk 28 optimal weight:   20.0000
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   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 336 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 = 0.3915 r_free = 0.3915 target = 0.169925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124629 restraints weight = 2393.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.69
r_work: 0.3169 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   2320  Z= 0.105
  Angle     :  0.515   6.603   3155  Z= 0.250
  Chirality :  0.037   0.121    381
  Planarity :  0.004   0.043    383
  Dihedral  :  3.298  13.840    311
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 36.29 %
    Favored  : 58.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.52), residues: 281
  helix:  1.91 (0.39), residues: 192
  sheet: -1.14 (1.30), residues: 18
  loop : -1.56 (0.71), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 153 
 TYR   0.008   0.001   TYR A 280 
 PHE   0.008   0.001   PHE A 269 
 TRP   0.005   0.001   TRP A 105 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2318)
  covalent geometry    : angle       0.51498 ( 3151)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.39510 (    4)
  hydrogen bonds       : bond        0.03477 (  137)
  hydrogen bonds       : angle       3.73595 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7005 (ttm170)
REVERT: A  108 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8110 (tttm)
REVERT: A  201 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.6975 (ttm110)
REVERT: A  233 ASP cc_start: 0.7855 (m-30) cc_final: 0.7593 (m-30)
REVERT: A  262 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8083 (ttm-80)
REVERT: A  331 LEU cc_start: 0.6694 (mt) cc_final: 0.6480 (mp)
REVERT: A  334 ARG cc_start: 0.7445 (tmm-80) cc_final: 0.6896 (tmm160)
  outliers start: 14
  outliers final: 9
  residues processed: 37
  average time/residue: 0.0981
  time to fit residues: 4.0773
Evaluate side-chains
  31 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  318 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 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 = 0.3796 r_free = 0.3796 target = 0.160370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.114807 restraints weight = 2377.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.63
r_work: 0.3129 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2320  Z= 0.120
  Angle     :  0.526   6.611   3155  Z= 0.258
  Chirality :  0.037   0.122    381
  Planarity :  0.004   0.039    383
  Dihedral  :  3.338  14.072    311
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 36.29 %
    Favored  : 58.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.52), residues: 281
  helix:  1.85 (0.38), residues: 192
  sheet: -1.05 (1.30), residues: 18
  loop : -1.56 (0.70), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 153 
 TYR   0.011   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2318)
  covalent geometry    : angle       0.52578 ( 3151)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.50903 (    4)
  hydrogen bonds       : bond        0.03948 (  137)
  hydrogen bonds       : angle       3.79034 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 24
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7067 (ttm110)
REVERT: A  233 ASP cc_start: 0.7911 (m-30) cc_final: 0.7659 (m-30)
REVERT: A  334 ARG cc_start: 0.7449 (tmm-80) cc_final: 0.6883 (tmm160)
  outliers start: 13
  outliers final: 12
  residues processed: 36
  average time/residue: 0.0908
  time to fit residues: 3.7396
Evaluate side-chains
  35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 23
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  318 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0570
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7702

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.159471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.113220 restraints weight = 2364.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.73
r_work: 0.3125 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2320  Z= 0.119
  Angle     :  0.543   8.081   3155  Z= 0.260
  Chirality :  0.037   0.121    381
  Planarity :  0.004   0.035    383
  Dihedral  :  3.314  14.280    311
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 35.89 %
    Favored  : 58.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.51), residues: 281
  helix:  1.88 (0.38), residues: 194
  sheet: -0.94 (1.30), residues: 18
  loop : -1.47 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2318)
  covalent geometry    : angle       0.54306 ( 3151)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.51333 (    4)
  hydrogen bonds       : bond        0.03811 (  137)
  hydrogen bonds       : angle       3.77187 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7077 (ttm110)
REVERT: A  233 ASP cc_start: 0.7988 (m-30) cc_final: 0.7723 (m-30)
REVERT: A  334 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.6914 (tmm160)
  outliers start: 14
  outliers final: 12
  residues processed: 37
  average time/residue: 0.0896
  time to fit residues: 3.7413
Evaluate side-chains
  36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  318 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.159522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.114283 restraints weight = 2413.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.70
r_work: 0.3145 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2320  Z= 0.112
  Angle     :  0.527   6.968   3155  Z= 0.253
  Chirality :  0.037   0.120    381
  Planarity :  0.004   0.034    383
  Dihedral  :  3.246  14.159    311
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 35.48 %
    Favored  : 58.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.51), residues: 281
  helix:  1.97 (0.38), residues: 194
  sheet: -0.82 (1.28), residues: 18
  loop : -1.41 (0.70), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.011   0.001   TYR A 280 
 PHE   0.009   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2318)
  covalent geometry    : angle       0.52713 ( 3151)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.49652 (    4)
  hydrogen bonds       : bond        0.03691 (  137)
  hydrogen bonds       : angle       3.73695 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 24
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7124 (ttm110)
REVERT: A  233 ASP cc_start: 0.7874 (m-30) cc_final: 0.7621 (m-30)
REVERT: A  334 ARG cc_start: 0.7466 (tmm-80) cc_final: 0.6896 (tmm160)
  outliers start: 15
  outliers final: 14
  residues processed: 38
  average time/residue: 0.1011
  time to fit residues: 4.3236
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.158239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.111582 restraints weight = 2366.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.72
r_work: 0.3108 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2320  Z= 0.139
  Angle     :  0.558   6.870   3155  Z= 0.270
  Chirality :  0.038   0.123    381
  Planarity :  0.004   0.035    383
  Dihedral  :  3.425  14.413    311
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 34.68 %
    Favored  : 58.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.51), residues: 281
  helix:  1.93 (0.38), residues: 192
  sheet: -0.68 (1.29), residues: 18
  loop : -1.61 (0.69), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.012   0.001   TYR A 280 
 PHE   0.011   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2318)
  covalent geometry    : angle       0.55773 ( 3151)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       0.63689 (    4)
  hydrogen bonds       : bond        0.04279 (  137)
  hydrogen bonds       : angle       3.86366 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 22
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  189 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.6107 (m-80)
REVERT: A  201 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7151 (ttm110)
REVERT: A  233 ASP cc_start: 0.8030 (m-30) cc_final: 0.7775 (m-30)
REVERT: A  334 ARG cc_start: 0.7429 (tmm-80) cc_final: 0.6896 (tmm160)
  outliers start: 16
  outliers final: 15
  residues processed: 37
  average time/residue: 0.0891
  time to fit residues: 3.7593
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 22
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0020
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.167401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.123247 restraints weight = 2400.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.60
r_work: 0.3154 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2320  Z= 0.110
  Angle     :  0.520   6.586   3155  Z= 0.251
  Chirality :  0.037   0.122    381
  Planarity :  0.004   0.033    383
  Dihedral  :  3.286  14.196    311
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 34.68 %
    Favored  : 59.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.51), residues: 281
  helix:  2.10 (0.38), residues: 192
  sheet: -0.64 (1.28), residues: 18
  loop : -1.60 (0.69), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.009   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 2318)
  covalent geometry    : angle       0.52033 ( 3151)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.46354 (    4)
  hydrogen bonds       : bond        0.03635 (  137)
  hydrogen bonds       : angle       3.74387 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  189 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.6107 (m-80)
REVERT: A  201 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7147 (ttm110)
REVERT: A  233 ASP cc_start: 0.7965 (m-30) cc_final: 0.7701 (m-30)
REVERT: A  334 ARG cc_start: 0.7437 (tmm-80) cc_final: 0.6904 (tmm160)
  outliers start: 15
  outliers final: 13
  residues processed: 37
  average time/residue: 0.0740
  time to fit residues: 3.1656
Evaluate side-chains
  37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 23
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  318 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 25 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.166472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.122451 restraints weight = 2404.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.61
r_work: 0.3145 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2320  Z= 0.119
  Angle     :  0.531   6.540   3155  Z= 0.257
  Chirality :  0.037   0.121    381
  Planarity :  0.004   0.033    383
  Dihedral  :  3.308  14.279    311
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 34.68 %
    Favored  : 59.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.51), residues: 281
  helix:  2.09 (0.38), residues: 192
  sheet: -0.71 (1.28), residues: 18
  loop : -1.62 (0.69), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.011   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 2318)
  covalent geometry    : angle       0.53076 ( 3151)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.51571 (    4)
  hydrogen bonds       : bond        0.03841 (  137)
  hydrogen bonds       : angle       3.77327 (  408)

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

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

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  562 Ramachandran restraints generated.
    281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  189 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.6153 (m-80)
REVERT: A  201 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7175 (ttm110)
REVERT: A  233 ASP cc_start: 0.7972 (m-30) cc_final: 0.7711 (m-30)
REVERT: A  334 ARG cc_start: 0.7452 (tmm-80) cc_final: 0.6912 (tmm160)
  outliers start: 15
  outliers final: 14
  residues processed: 36
  average time/residue: 0.0645
  time to fit residues: 2.6890
Evaluate side-chains
  37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   72 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0170
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5618

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.166300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122118 restraints weight = 2417.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.62
r_work: 0.3159 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   2320  Z= 0.107
  Angle     :  0.515   6.466   3155  Z= 0.248
  Chirality :  0.037   0.118    381
  Planarity :  0.004   0.033    383
  Dihedral  :  3.220  14.090    311
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 33.87 %
    Favored  : 59.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.51), residues: 281
  helix:  2.17 (0.38), residues: 192
  sheet: -0.74 (1.27), residues: 18
  loop : -1.60 (0.69), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.002   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 2318)
  covalent geometry    : angle       0.51487 ( 3151)
  SS BOND              : bond        0.00058 (    2)
  SS BOND              : angle       0.45087 (    4)
  hydrogen bonds       : bond        0.03499 (  137)
  hydrogen bonds       : angle       3.69188 (  408)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 895.10 seconds
wall clock time: 15 minutes 55.51 seconds (955.51 seconds total)