Starting phenix.real_space_refine
on Fri Aug 22 13:03:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zms_60255/08_2025/8zms_60255.cif"
  }
  resolution = 3.7
  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=   0.020
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      17      5.16       5
     C    1940      2.51       5
     N     463      2.21       5
     O     500      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2920
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 2910
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 24, 'TRANS': 361}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'ACH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.81, per 1000 atoms: 0.28
  Number of scatterers: 2920
  At special positions: 0
  Unit cell: (70.55, 59.76, 83.83, 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      17     16.00
     O     500      8.00
     N     463      7.00
     C    1940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 123.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  716

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      88.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 54
      removed outlier: 3.608A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   VAL A  54 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 4.051A  pdb=" N   ILE A  61 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 149
      removed outlier: 3.577A  pdb=" N   ASN A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 151 through 171
      removed outlier: 3.749A  pdb=" N   PHE A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 201
      removed outlier: 4.660A  pdb=" N   THR A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   SER A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 238
      Proline residue:  A 229  - end of helix
      removed outlier: 4.174A  pdb=" N   LEU A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 264
      removed outlier: 3.849A  pdb=" N   PHE A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 307
      Proline residue:  A 304  - end of helix
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.676A  pdb=" N   TRP A 315 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 329
    Processing helix  chain 'A' and resid 331 through 334
      removed outlier: 3.580A  pdb=" N   ALA A 334 " --> pdb=" O   TRP A 331 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 331 through 334'
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 355 through 374
      removed outlier: 3.529A  pdb=" N   TYR A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL A 374 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 379 through 413
      removed outlier: 3.900A  pdb=" N   LEU A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      Proline residue:  A 403  - end of helix
    Processing helix  chain 'A' and resid 418 through 446
      removed outlier: 4.151A  pdb=" N   ALA A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      Proline residue:  A 436  - end of helix
      removed outlier: 4.386A  pdb=" N   GLY A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   HIS A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 463
    Processing helix  chain 'A' and resid 464 through 469
      removed outlier: 3.774A  pdb=" N   LEU A 467 " --> pdb=" O   PRO A 464 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 468 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 464 through 469'

    229 hydrogen bonds defined for protein.
    681 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: 0.34

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 450
        1.31 -     1.43: 765
        1.43 -     1.56: 1746
        1.56 -     1.68: 0
        1.68 -     1.81: 28
  Bond restraints: 2989
  Sorted by residual:
  bond pdb=" C5  ACH A1001 "
       pdb=" O4  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.410 -0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" C2  ACH A1001 "
       pdb=" C3  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.509  1.553 -0.044 2.00e-02 2.50e+03 4.86e+00
  bond pdb=" C5  ACH A1001 "
       pdb=" C6  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.497  1.541 -0.044 2.00e-02 2.50e+03 4.82e+00
  bond pdb=" CA  VAL A 336 "
       pdb=" C   VAL A 336 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 8.80e-03 1.29e+04 3.04e+00
  bond pdb=" C   ILE A 303 "
       pdb=" N   PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.23e-02 6.61e+03 2.99e+00
  ... (remaining 2984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 3867
        2.14 -     4.29: 157
        4.29 -     6.43: 37
        6.43 -     8.58: 17
        8.58 -    10.72: 4
  Bond angle restraints: 4082
  Sorted by residual:
  angle pdb=" C   PHE A 335 "
        pdb=" N   VAL A 336 "
        pdb=" CA  VAL A 336 "
      ideal   model   delta    sigma   weight residual
     120.24  123.54   -3.30 6.30e-01 2.52e+00 2.74e+01
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" C   PRO A 229 "
      ideal   model   delta    sigma   weight residual
     110.70  115.83   -5.13 1.22e+00 6.72e-01 1.77e+01
  angle pdb=" CA  PRO A 229 "
        pdb=" C   PRO A 229 "
        pdb=" N   PRO A 230 "
      ideal   model   delta    sigma   weight residual
     117.93  122.77   -4.84 1.20e+00 6.94e-01 1.63e+01
  angle pdb=" N   VAL A 374 "
        pdb=" CA  VAL A 374 "
        pdb=" C   VAL A 374 "
      ideal   model   delta    sigma   weight residual
     108.88  116.63   -7.75 2.16e+00 2.14e-01 1.29e+01
  angle pdb=" C10 ACH A1001 "
        pdb=" N1  ACH A1001 "
        pdb=" C9  ACH A1001 "
      ideal   model   delta    sigma   weight residual
     108.54  119.26  -10.72 3.00e+00 1.11e-01 1.28e+01
  ... (remaining 4077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.28: 1595
       11.28 -    22.57: 128
       22.57 -    33.85: 26
       33.85 -    45.13: 10
       45.13 -    56.42: 3
  Dihedral angle restraints: 1762
    sinusoidal: 648
      harmonic: 1114
  Sorted by residual:
  dihedral pdb=" CA  SER A 379 "
           pdb=" C   SER A 379 "
           pdb=" N   PHE A 380 "
           pdb=" CA  PHE A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASP A 288 "
           pdb=" C   ASP A 288 "
           pdb=" N   PRO A 289 "
           pdb=" CA  PRO A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  GLU A 206 "
           pdb=" C   GLU A 206 "
           pdb=" N   GLU A 207 "
           pdb=" CA  GLU A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.46  -17.54     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1759 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 341
       0.049 -    0.098: 113
       0.098 -    0.147: 36
       0.147 -    0.195: 6
       0.195 -    0.244: 1
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" CB  VAL A  54 "
            pdb=" CA  VAL A  54 "
            pdb=" CG1 VAL A  54 "
            pdb=" CG2 VAL A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CG  LEU A 178 "
            pdb=" CB  LEU A 178 "
            pdb=" CD1 LEU A 178 "
            pdb=" CD2 LEU A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  ASN A 139 "
            pdb=" N   ASN A 139 "
            pdb=" C   ASN A 139 "
            pdb=" CB  ASN A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.30e-01
  ... (remaining 494 not shown)

  Planarity restraints: 501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 309 "    0.044 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 310 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 224 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.69e+00
        pdb=" C   GLY A 224 "    0.041 2.00e-02 2.50e+03
        pdb=" O   GLY A 224 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 225 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 228 "    0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 229 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "    0.031 5.00e-02 4.00e+02
  ... (remaining 498 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 931
        2.86 -     3.37: 2895
        3.37 -     3.88: 4862
        3.88 -     4.39: 5087
        4.39 -     4.90: 8758
  Nonbonded interactions: 22533
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 127 "
            pdb=" OG  SER A 130 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   ASP A 174 "
            pdb=" OG1 THR A 177 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OD2 ASP A 147 "
            pdb=" OG  SER A 419 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" ND2 ASN A 139 "
            pdb=" OD2 ASP A 425 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   GLN A 135 "
            pdb=" ND2 ASN A 139 "
     model   vdw
     2.412 3.120
  ... (remaining 22528 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.040
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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      :  0.007   0.075   2989  Z= 0.287
  Angle     :  1.147  10.721   4082  Z= 0.589
  Chirality :  0.055   0.244    497
  Planarity :  0.010   0.066    501
  Dihedral  :  9.676  56.418   1046
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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: -3.71 (0.32), residues: 380
  helix: -2.04 (0.21), residues: 301
  sheet:  None (None), residues: 0
  loop : -3.30 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 378 
 TYR   0.014   0.002   TYR A  50 
 PHE   0.019   0.003   PHE A 238 
 TRP   0.022   0.002   TRP A 325 
 HIS   0.005   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 2989)
  covalent geometry    : angle       1.14655 ( 4082)
  hydrogen bonds       : bond        0.11269 (  229)
  hydrogen bonds       : angle       5.80500 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7771 (tt0) cc_final: 0.7280 (pm20)
REVERT: A  254 PHE cc_start: 0.7232 (t80) cc_final: 0.7026 (m-80)
REVERT: A  286 MET cc_start: 0.5604 (mmp) cc_final: 0.4183 (ttm)
REVERT: A  305 LEU cc_start: 0.8372 (mt) cc_final: 0.8097 (mt)
REVERT: A  429 SER cc_start: 0.8595 (m) cc_final: 0.8097 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0557
  time to fit residues: 6.1275
Evaluate side-chains
  65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.182430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.167131 restraints weight = 4645.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.170931 restraints weight = 2501.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.173376 restraints weight = 1557.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.175154 restraints weight = 1077.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.176411 restraints weight = 794.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2989  Z= 0.150
  Angle     :  0.713   7.176   4082  Z= 0.350
  Chirality :  0.041   0.135    497
  Planarity :  0.006   0.047    501
  Dihedral  :  5.763  46.447    415
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.42 %
    Favored  : 85.95 %
  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 (0.41), residues: 380
  helix: -0.07 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.32 (0.68), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.011   0.002   TYR A 352 
 PHE   0.028   0.002   PHE A 169 
 TRP   0.012   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2989)
  covalent geometry    : angle       0.71309 ( 4082)
  hydrogen bonds       : bond        0.04345 (  229)
  hydrogen bonds       : angle       4.29054 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7678 (tt0) cc_final: 0.7397 (pm20)
REVERT: A  286 MET cc_start: 0.5464 (mmp) cc_final: 0.4095 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.0340
  time to fit residues: 3.3326
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  278 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0060
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.4078 r_free = 0.4078 target = 0.179855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.164263 restraints weight = 4677.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168208 restraints weight = 2482.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.170738 restraints weight = 1534.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172480 restraints weight = 1053.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.173728 restraints weight = 780.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2989  Z= 0.141
  Angle     :  0.684   7.119   4082  Z= 0.334
  Chirality :  0.040   0.117    497
  Planarity :  0.005   0.039    501
  Dihedral  :  5.416  41.871    415
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.71 %
    Favored  : 81.37 %
  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:  0.13 (0.44), residues: 380
  helix:  0.79 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -3.05 (0.66), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 428 
 PHE   0.023   0.002   PHE A 169 
 TRP   0.009   0.001   TRP A 325 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2989)
  covalent geometry    : angle       0.68376 ( 4082)
  hydrogen bonds       : bond        0.04018 (  229)
  hydrogen bonds       : angle       4.08280 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7680 (tt0) cc_final: 0.7388 (pm20)
REVERT: A  286 MET cc_start: 0.5599 (mmp) cc_final: 0.4160 (ttp)
REVERT: A  299 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8365 (m)
REVERT: A  410 ASP cc_start: 0.8203 (m-30) cc_final: 0.7925 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 0.0276
  time to fit residues: 2.8431
Evaluate side-chains
  67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  299 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0770
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0270
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.180293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.165017 restraints weight = 4671.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.168831 restraints weight = 2488.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.171475 restraints weight = 1544.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.173180 restraints weight = 1052.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.174450 restraints weight = 778.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2989  Z= 0.136
  Angle     :  0.673   8.118   4082  Z= 0.326
  Chirality :  0.040   0.129    497
  Planarity :  0.005   0.037    501
  Dihedral  :  5.236  41.553    415
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.71 %
    Favored  : 82.03 %
  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:  0.59 (0.45), residues: 380
  helix:  1.04 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.88 (0.75), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.008   0.001   TYR A 359 
 PHE   0.021   0.001   PHE A 169 
 TRP   0.009   0.001   TRP A 357 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2989)
  covalent geometry    : angle       0.67316 ( 4082)
  hydrogen bonds       : bond        0.03790 (  229)
  hydrogen bonds       : angle       3.97192 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7656 (tt0) cc_final: 0.7384 (pm20)
REVERT: A   51 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7389 (mmm)
REVERT: A  286 MET cc_start: 0.5665 (mmp) cc_final: 0.4183 (tmm)
REVERT: A  311 THR cc_start: 0.9219 (m) cc_final: 0.8800 (t)
REVERT: A  410 ASP cc_start: 0.8223 (m-30) cc_final: 0.7953 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0305
  time to fit residues: 2.9305
Evaluate side-chains
  68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0170
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.177363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.162251 restraints weight = 4610.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.165987 restraints weight = 2505.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.168548 restraints weight = 1577.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170319 restraints weight = 1092.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.171416 restraints weight = 803.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2989  Z= 0.155
  Angle     :  0.707   8.943   4082  Z= 0.341
  Chirality :  0.042   0.150    497
  Planarity :  0.005   0.036    501
  Dihedral  :  5.274  41.479    415
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 15.36 %
    Favored  : 79.74 %
  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:  0.66 (0.45), residues: 380
  helix:  1.09 (0.30), residues: 316
  sheet:  None (None), residues: 0
  loop : -2.72 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.011   0.002   TYR A 432 
 PHE   0.018   0.002   PHE A 169 
 TRP   0.011   0.002   TRP A 357 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2989)
  covalent geometry    : angle       0.70683 ( 4082)
  hydrogen bonds       : bond        0.03976 (  229)
  hydrogen bonds       : angle       4.02095 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7759 (tt0) cc_final: 0.7465 (pm20)
REVERT: A  124 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7734 (mt)
REVERT: A  286 MET cc_start: 0.5746 (mmp) cc_final: 0.4304 (ttp)
REVERT: A  410 ASP cc_start: 0.8314 (m-30) cc_final: 0.8025 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0295
  time to fit residues: 2.7790
Evaluate side-chains
  67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.178108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163072 restraints weight = 4625.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.167026 restraints weight = 2467.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.169673 restraints weight = 1517.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171395 restraints weight = 1023.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.172594 restraints weight = 743.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2989  Z= 0.145
  Angle     :  0.688   8.215   4082  Z= 0.334
  Chirality :  0.042   0.162    497
  Planarity :  0.005   0.037    501
  Dihedral  :  5.193  40.965    415
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.65 %
    Favored  : 78.76 %
  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:  0.84 (0.45), residues: 380
  helix:  1.19 (0.30), residues: 316
  sheet:  None (None), residues: 0
  loop : -2.58 (0.78), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 432 
 PHE   0.018   0.001   PHE A 169 
 TRP   0.013   0.001   TRP A 357 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2989)
  covalent geometry    : angle       0.68800 ( 4082)
  hydrogen bonds       : bond        0.03850 (  229)
  hydrogen bonds       : angle       4.00042 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7772 (tt0) cc_final: 0.7468 (pm20)
REVERT: A   51 MET cc_start: 0.8129 (mmm) cc_final: 0.7901 (mmt)
REVERT: A  124 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7742 (mt)
REVERT: A  286 MET cc_start: 0.5778 (mmp) cc_final: 0.4245 (ttp)
REVERT: A  410 ASP cc_start: 0.8355 (m-30) cc_final: 0.8039 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0465
  time to fit residues: 4.0151
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0060
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0070
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0970
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.2612

-------------------------------------------------------------------------------
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 = 0.4113 r_free = 0.4113 target = 0.183206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.167943 restraints weight = 4625.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.172102 restraints weight = 2470.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.174794 restraints weight = 1509.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.176482 restraints weight = 1007.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.177700 restraints weight = 729.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2989  Z= 0.131
  Angle     :  0.654   7.681   4082  Z= 0.319
  Chirality :  0.040   0.138    497
  Planarity :  0.005   0.037    501
  Dihedral  :  4.962  37.834    415
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.30 %
    Favored  : 78.43 %
  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:  1.07 (0.46), residues: 380
  helix:  1.40 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.74 (0.81), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 212 
 TYR   0.012   0.001   TYR A  50 
 PHE   0.016   0.001   PHE A 169 
 TRP   0.016   0.001   TRP A 357 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2989)
  covalent geometry    : angle       0.65440 ( 4082)
  hydrogen bonds       : bond        0.03459 (  229)
  hydrogen bonds       : angle       3.88092 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7639 (tt0) cc_final: 0.7397 (pm20)
REVERT: A  278 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7966 (t)
REVERT: A  286 MET cc_start: 0.5831 (mmp) cc_final: 0.4285 (tmm)
REVERT: A  332 LEU cc_start: 0.8361 (tt) cc_final: 0.8073 (tp)
REVERT: A  410 ASP cc_start: 0.8387 (m-30) cc_final: 0.8077 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0239
  time to fit residues: 2.2511
Evaluate side-chains
  62 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 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 = 0.4094 r_free = 0.4094 target = 0.181618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166430 restraints weight = 4741.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170311 restraints weight = 2564.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172936 restraints weight = 1592.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.174580 restraints weight = 1075.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.175832 restraints weight = 792.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2989  Z= 0.154
  Angle     :  0.700   7.170   4082  Z= 0.340
  Chirality :  0.042   0.148    497
  Planarity :  0.005   0.035    501
  Dihedral  :  5.325  50.286    415
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.63 %
    Favored  : 79.41 %
  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:  0.96 (0.45), residues: 380
  helix:  1.28 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.54 (0.81), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.011   0.001   TYR A  50 
 PHE   0.015   0.002   PHE A 169 
 TRP   0.016   0.002   TRP A 357 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 2989)
  covalent geometry    : angle       0.69998 ( 4082)
  hydrogen bonds       : bond        0.03868 (  229)
  hydrogen bonds       : angle       3.99283 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7761 (tt0) cc_final: 0.7490 (pm20)
REVERT: A   51 MET cc_start: 0.7947 (mmm) cc_final: 0.7686 (mmt)
REVERT: A  286 MET cc_start: 0.5879 (mmp) cc_final: 0.4280 (ttp)
REVERT: A  332 LEU cc_start: 0.8371 (tt) cc_final: 0.8125 (tp)
REVERT: A  410 ASP cc_start: 0.8355 (m-30) cc_final: 0.8057 (m-30)
  outliers start: 6
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0302
  time to fit residues: 2.6099
Evaluate side-chains
  62 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.180360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.165077 restraints weight = 4676.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.169133 restraints weight = 2484.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.171659 restraints weight = 1512.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173458 restraints weight = 1023.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.174619 restraints weight = 742.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2989  Z= 0.141
  Angle     :  0.693   7.314   4082  Z= 0.335
  Chirality :  0.041   0.137    497
  Planarity :  0.005   0.037    501
  Dihedral  :  5.211  47.373    415
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.99 %
    Favored  : 80.07 %
  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:  0.99 (0.45), residues: 380
  helix:  1.33 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -2.47 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.014   0.001   TYR A  50 
 PHE   0.015   0.001   PHE A 169 
 TRP   0.018   0.002   TRP A 357 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2989)
  covalent geometry    : angle       0.69283 ( 4082)
  hydrogen bonds       : bond        0.03795 (  229)
  hydrogen bonds       : angle       3.97302 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7798 (tt0) cc_final: 0.7491 (pm20)
REVERT: A  286 MET cc_start: 0.5920 (mmp) cc_final: 0.4295 (ttp)
REVERT: A  332 LEU cc_start: 0.8372 (tt) cc_final: 0.8114 (tp)
REVERT: A  410 ASP cc_start: 0.8385 (m-30) cc_final: 0.8077 (m-30)
  outliers start: 9
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0251
  time to fit residues: 2.2804
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   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 135 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 = 0.4071 r_free = 0.4071 target = 0.179077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.163850 restraints weight = 4732.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167725 restraints weight = 2562.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.170321 restraints weight = 1592.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.171967 restraints weight = 1082.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.173180 restraints weight = 801.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2989  Z= 0.152
  Angle     :  0.732   9.628   4082  Z= 0.349
  Chirality :  0.042   0.154    497
  Planarity :  0.005   0.034    501
  Dihedral  :  5.309  48.264    415
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.65 %
    Favored  : 79.41 %
  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:  0.94 (0.45), residues: 380
  helix:  1.29 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -2.45 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.013   0.001   TYR A  50 
 PHE   0.013   0.001   PHE A 169 
 TRP   0.020   0.002   TRP A 357 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 2989)
  covalent geometry    : angle       0.73197 ( 4082)
  hydrogen bonds       : bond        0.03952 (  229)
  hydrogen bonds       : angle       4.01182 (  681)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7814 (tt0) cc_final: 0.7519 (pm20)
REVERT: A  286 MET cc_start: 0.5960 (mmp) cc_final: 0.4563 (ttt)
REVERT: A  332 LEU cc_start: 0.8424 (tt) cc_final: 0.8161 (tp)
REVERT: A  410 ASP cc_start: 0.8339 (m-30) cc_final: 0.8055 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0222
  time to fit residues: 1.9090
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0570
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.180180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.164866 restraints weight = 4736.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.168865 restraints weight = 2559.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.171447 restraints weight = 1584.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.173164 restraints weight = 1076.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.174356 restraints weight = 790.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2989  Z= 0.143
  Angle     :  0.724  11.432   4082  Z= 0.342
  Chirality :  0.041   0.144    497
  Planarity :  0.005   0.033    501
  Dihedral  :  5.266  48.442    415
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.30 %
    Favored  : 79.08 %
  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:  1.02 (0.45), residues: 380
  helix:  1.34 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -2.39 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.014   0.001   TYR A  50 
 PHE   0.014   0.001   PHE A 169 
 TRP   0.019   0.002   TRP A 357 
 HIS   0.002   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2989)
  covalent geometry    : angle       0.72352 ( 4082)
  hydrogen bonds       : bond        0.03807 (  229)
  hydrogen bonds       : angle       3.95850 (  681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 644.23 seconds
wall clock time: 11 minutes 44.81 seconds (704.81 seconds total)