Starting phenix.real_space_refine
on Wed Sep 17 04:37:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mgk_48261/09_2025/9mgk_48261.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.002
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      36      5.16       5
     C    2727      2.51       5
     N     655      2.21       5
     O     717      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 4135
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4049
          Classifications: {'peptide': 528}
          Link IDs: {'PTRANS': 28, 'TRANS': 499}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'AJP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 198
          Unresolved non-hydrogen chiralities: 38
  Time building chain proxies: 1.29, per 1000 atoms: 0.31
  Number of scatterers: 4135
  At special positions: 0
  Unit cell: (101.004, 60.248, 76.196, 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      36     16.00
     O     717      8.00
     N     655      7.00
     C    2727      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 143 " - pdb=" SG  CYS A 448 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 420 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 594 " 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: 0.42
  Conformation dependent library (CDL) restraints added in 123.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  980

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 2 sheets defined
      70.1% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 28
      removed outlier: 4.437A  pdb=" N   PHE A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 56
      removed outlier: 3.605A  pdb=" N   PHE A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.681A  pdb=" N   ILE A  83 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 122
      Proline residue:  A 118  - end of helix
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 186 through 198
      removed outlier: 3.776A  pdb=" N   PHE A 190 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   SER A 193 " --> pdb=" O   PRO A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 202
      No H-bonds generated for 'chain 'A' and resid 200 through 202'
    Processing helix  chain 'A' and resid 203 through 228
      removed outlier: 4.049A  pdb=" N   TYR A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 257 through 273
    Processing helix  chain 'A' and resid 274 through 276
      No H-bonds generated for 'chain 'A' and resid 274 through 276'
    Processing helix  chain 'A' and resid 310 through 313
    Processing helix  chain 'A' and resid 314 through 325
      removed outlier: 3.658A  pdb=" N   LEU A 323 " --> pdb=" O   PHE A 319 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 325 " --> pdb=" O   ARG A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 348
    Processing helix  chain 'A' and resid 348 through 357
    Processing helix  chain 'A' and resid 360 through 371
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'A' and resid 396 through 413
    Processing helix  chain 'A' and resid 442 through 447
      removed outlier: 4.048A  pdb=" N   ASP A 447 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 515 through 543
      removed outlier: 3.707A  pdb=" N   ASN A 534 " --> pdb=" O   CYS A 530 " (cutoff:3.500A)
      Proline residue:  A 535  - end of helix
    Processing helix  chain 'A' and resid 545 through 565
    Processing helix  chain 'A' and resid 566 through 579
      removed outlier: 4.015A  pdb=" N   ALA A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 629
      removed outlier: 3.982A  pdb=" N   ARG A 603 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASP A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A 609 " --> pdb=" O   ARG A 605 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 474 through 478
      removed outlier: 5.913A  pdb=" N   CYS A 474 " --> pdb=" O   CYS A 492 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   CYS A 492 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 488 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 582
      removed outlier: 3.906A  pdb=" N   TYR A 596 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    771 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: 0.59

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1228
        1.35 -     1.47: 1079
        1.47 -     1.58: 1891
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 4248
  Sorted by residual:
  bond pdb=" N   THR A 504 "
       pdb=" CA  THR A 504 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.09e+00
  bond pdb=" C   PHE A 315 "
       pdb=" N   PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.015 1.51e-02 4.39e+03 9.65e-01
  bond pdb=" CB  MET A 538 "
       pdb=" CG  MET A 538 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.92e-01
  bond pdb=" SD  MET A 538 "
       pdb=" CE  MET A 538 "
    ideal  model  delta    sigma   weight residual
    1.791  1.768  0.023 2.50e-02 1.60e+03 8.60e-01
  bond pdb=" N   PRO A 510 "
       pdb=" CA  PRO A 510 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 8.55e-01
  ... (remaining 4243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 5476
        1.37 -     2.74: 248
        2.74 -     4.11: 45
        4.11 -     5.48: 21
        5.48 -     6.85: 8
  Bond angle restraints: 5798
  Sorted by residual:
  angle pdb=" N   ASP A 310 "
        pdb=" CA  ASP A 310 "
        pdb=" C   ASP A 310 "
      ideal   model   delta    sigma   weight residual
     114.56  110.64    3.92 1.27e+00 6.20e-01 9.52e+00
  angle pdb=" C   ARG A 314 "
        pdb=" N   PHE A 315 "
        pdb=" CA  PHE A 315 "
      ideal   model   delta    sigma   weight residual
     120.58  124.58   -4.00 1.32e+00 5.74e-01 9.20e+00
  angle pdb=" CB  LYS A 355 "
        pdb=" CG  LYS A 355 "
        pdb=" CD  LYS A 355 "
      ideal   model   delta    sigma   weight residual
     111.30  104.45    6.85 2.30e+00 1.89e-01 8.87e+00
  angle pdb=" C   THR A 504 "
        pdb=" N   GLY A 505 "
        pdb=" CA  GLY A 505 "
      ideal   model   delta    sigma   weight residual
     121.58  119.18    2.40 8.60e-01 1.35e+00 7.78e+00
  angle pdb=" N   TYR A 429 "
        pdb=" CA  TYR A 429 "
        pdb=" C   TYR A 429 "
      ideal   model   delta    sigma   weight residual
     109.81  115.57   -5.76 2.21e+00 2.05e-01 6.79e+00
  ... (remaining 5793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.09: 2436
       18.09 -    36.18: 216
       36.18 -    54.27: 35
       54.27 -    72.36: 4
       72.36 -    90.45: 5
  Dihedral angle restraints: 2696
    sinusoidal: 1176
      harmonic: 1520
  Sorted by residual:
  dihedral pdb=" CB  CYS A 580 "
           pdb=" SG  CYS A 580 "
           pdb=" SG  CYS A 594 "
           pdb=" CB  CYS A 594 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.55  -90.45     1      1.00e+01 1.00e-02 9.68e+01
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 507 "
           pdb=" CB  CYS A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.68   67.32     1      1.00e+01 1.00e-02 5.90e+01
  dihedral pdb=" CB  CYS A 420 "
           pdb=" SG  CYS A 420 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.01   44.99     1      1.00e+01 1.00e-02 2.81e+01
  ... (remaining 2693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 509
       0.046 -    0.092: 146
       0.092 -    0.138: 34
       0.138 -    0.184: 6
       0.184 -    0.231: 2
  Chirality restraints: 697
  Sorted by residual:
  chirality pdb=" CG  LEU A 330 "
            pdb=" CB  LEU A 330 "
            pdb=" CD1 LEU A 330 "
            pdb=" CD2 LEU A 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  VAL A 544 "
            pdb=" CA  VAL A 544 "
            pdb=" CG1 VAL A 544 "
            pdb=" CG2 VAL A 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  VAL A 185 "
            pdb=" N   VAL A 185 "
            pdb=" C   VAL A 185 "
            pdb=" CB  VAL A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.27    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 694 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 185 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 186 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 186 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 186 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 273 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO A 274 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 274 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 274 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 188 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO A 189 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 167
        2.72 -     3.27: 4577
        3.27 -     3.81: 7045
        3.81 -     4.36: 7630
        4.36 -     4.90: 13013
  Nonbonded interactions: 32432
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 119 "
            pdb=" OG  SER A 122 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   THR A 403 "
            pdb=" OG1 THR A 406 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASN A 476 "
            pdb=" ND2 ASN A 491 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD2 ASP A 461 "
            pdb=" OG  SER A 499 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A 480 "
            pdb=" OG  SER A 484 "
     model   vdw
     2.288 3.040
  ... (remaining 32427 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:             2.810
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.160
  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:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
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      :  0.003   0.045   4255  Z= 0.155
  Angle     :  0.716   6.851   5812  Z= 0.361
  Chirality :  0.046   0.231    697
  Planarity :  0.005   0.050    696
  Dihedral  : 13.593  86.167   1695
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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:  0.85 (0.40), residues: 516
  helix:  1.46 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.07 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 627 
 TYR   0.011   0.001   TYR A 613 
 PHE   0.010   0.001   PHE A 275 
 TRP   0.011   0.001   TRP A 583 
 HIS   0.006   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4248)
  covalent geometry    : angle       0.71577 ( 5798)
  SS BOND              : bond        0.00180 (    7)
  SS BOND              : angle       0.92076 (   14)
  hydrogen bonds       : bond        0.11275 (  260)
  hydrogen bonds       : angle       4.94034 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.7427 (mttt) cc_final: 0.7110 (mttp)
REVERT: A  141 GLU cc_start: 0.7480 (mp0) cc_final: 0.7011 (mp0)
REVERT: A  318 ILE cc_start: 0.8850 (mp) cc_final: 0.8579 (mp)
REVERT: A  351 LYS cc_start: 0.8557 (tppt) cc_final: 0.8163 (tptm)
REVERT: A  387 MET cc_start: 0.8789 (tpp) cc_final: 0.8375 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0657
  time to fit residues: 7.9855
Evaluate side-chains
  77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.3980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4060 r_free = 0.4060 target = 0.183959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.162416 restraints weight = 6957.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.165242 restraints weight = 4487.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.167225 restraints weight = 3208.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.168589 restraints weight = 2475.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.169389 restraints weight = 2050.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.0784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4255  Z= 0.142
  Angle     :  0.672  10.686   5812  Z= 0.324
  Chirality :  0.044   0.162    697
  Planarity :  0.005   0.042    696
  Dihedral  :  5.725  40.680    801
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.58 %
    Favored  : 94.20 %
  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:  1.12 (0.40), residues: 516
  helix:  1.59 (0.30), residues: 330
  sheet:  None (None), residues: 0
  loop : -0.79 (0.52), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.008   0.001   TYR A 429 
 PHE   0.009   0.001   PHE A 275 
 TRP   0.008   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4248)
  covalent geometry    : angle       0.67121 ( 5798)
  SS BOND              : bond        0.00181 (    7)
  SS BOND              : angle       0.79094 (   14)
  hydrogen bonds       : bond        0.04188 (  260)
  hydrogen bonds       : angle       4.59647 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.7357 (mttt) cc_final: 0.6985 (mttp)
REVERT: A  141 GLU cc_start: 0.7370 (mp0) cc_final: 0.6930 (mp0)
REVERT: A  351 LYS cc_start: 0.8528 (tppt) cc_final: 0.8274 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0560
  time to fit residues: 6.7192
Evaluate side-chains
  69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0170
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 177 GLN
** A 350 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.183628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.161648 restraints weight = 6857.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.164667 restraints weight = 4404.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166725 restraints weight = 3113.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.168245 restraints weight = 2394.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.169243 restraints weight = 1955.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4255  Z= 0.135
  Angle     :  0.660   9.014   5812  Z= 0.318
  Chirality :  0.044   0.198    697
  Planarity :  0.004   0.043    696
  Dihedral  :  5.634  40.600    801
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.36 %
    Favored  : 94.42 %
  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:  1.11 (0.40), residues: 516
  helix:  1.57 (0.30), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.77 (0.53), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.008   0.001   TYR A 597 
 PHE   0.008   0.001   PHE A 557 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.003   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4248)
  covalent geometry    : angle       0.65954 ( 5798)
  SS BOND              : bond        0.00145 (    7)
  SS BOND              : angle       0.87171 (   14)
  hydrogen bonds       : bond        0.04052 (  260)
  hydrogen bonds       : angle       4.43206 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.7249 (mttt) cc_final: 0.7044 (mttm)
REVERT: A  141 GLU cc_start: 0.7314 (mp0) cc_final: 0.6891 (mp0)
REVERT: A  318 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8153 (mt)
REVERT: A  351 LYS cc_start: 0.8539 (tppt) cc_final: 0.8329 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0582
  time to fit residues: 6.8319
Evaluate side-chains
  71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   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  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 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 = 0.4060 r_free = 0.4060 target = 0.183934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.162013 restraints weight = 6664.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164972 restraints weight = 4260.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.166853 restraints weight = 3012.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.168402 restraints weight = 2337.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.169658 restraints weight = 1912.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4255  Z= 0.139
  Angle     :  0.678   6.722   5812  Z= 0.327
  Chirality :  0.044   0.154    697
  Planarity :  0.004   0.037    696
  Dihedral  :  5.630  40.351    801
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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:  1.12 (0.40), residues: 516
  helix:  1.56 (0.30), residues: 328
  sheet:  None (None), residues: 0
  loop : -0.71 (0.52), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  97 
 TYR   0.007   0.001   TYR A 613 
 PHE   0.027   0.001   PHE A 113 
 TRP   0.007   0.001   TRP A 583 
 HIS   0.003   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4248)
  covalent geometry    : angle       0.67746 ( 5798)
  SS BOND              : bond        0.00158 (    7)
  SS BOND              : angle       0.96568 (   14)
  hydrogen bonds       : bond        0.04000 (  260)
  hydrogen bonds       : angle       4.53366 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.7150 (mttt) cc_final: 0.6945 (mttm)
REVERT: A  141 GLU cc_start: 0.7320 (mp0) cc_final: 0.6879 (mp0)
REVERT: A  318 ILE cc_start: 0.8706 (mp) cc_final: 0.8298 (mt)
REVERT: A  351 LYS cc_start: 0.8590 (tppt) cc_final: 0.8226 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0668
  time to fit residues: 7.7736
Evaluate side-chains
  71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 48 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0270
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4044 r_free = 0.4044 target = 0.183479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.162841 restraints weight = 6830.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.165750 restraints weight = 4356.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.167836 restraints weight = 3071.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.168811 restraints weight = 2344.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.169779 restraints weight = 1984.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4255  Z= 0.130
  Angle     :  0.667   7.157   5812  Z= 0.319
  Chirality :  0.044   0.220    697
  Planarity :  0.004   0.035    696
  Dihedral  :  5.517  39.928    801
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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:  1.14 (0.40), residues: 516
  helix:  1.58 (0.30), residues: 328
  sheet:  None (None), residues: 0
  loop : -0.69 (0.52), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 321 
 TYR   0.016   0.001   TYR A 606 
 PHE   0.021   0.001   PHE A 113 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.003   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4248)
  covalent geometry    : angle       0.66600 ( 5798)
  SS BOND              : bond        0.00147 (    7)
  SS BOND              : angle       1.00868 (   14)
  hydrogen bonds       : bond        0.03814 (  260)
  hydrogen bonds       : angle       4.50432 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7241 (mp0) cc_final: 0.6813 (mp0)
REVERT: A  233 PHE cc_start: 0.6128 (t80) cc_final: 0.5915 (t80)
REVERT: A  318 ILE cc_start: 0.8645 (mp) cc_final: 0.8293 (mt)
REVERT: A  324 MET cc_start: 0.5913 (mtt) cc_final: 0.5447 (mtm)
REVERT: A  351 LYS cc_start: 0.8612 (tppt) cc_final: 0.8366 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0587
  time to fit residues: 6.9581
Evaluate side-chains
  78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0980
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4040 r_free = 0.4040 target = 0.183331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.162454 restraints weight = 7031.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.165601 restraints weight = 4469.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.167774 restraints weight = 3115.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.169195 restraints weight = 2361.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.170361 restraints weight = 1920.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4255  Z= 0.129
  Angle     :  0.670   9.755   5812  Z= 0.316
  Chirality :  0.044   0.181    697
  Planarity :  0.004   0.034    696
  Dihedral  :  5.487  39.850    801
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  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 (0.40), residues: 516
  helix:  1.66 (0.30), residues: 328
  sheet:  None (None), residues: 0
  loop : -0.56 (0.52), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 252 
 TYR   0.013   0.001   TYR A 606 
 PHE   0.016   0.001   PHE A 113 
 TRP   0.007   0.001   TRP A 583 
 HIS   0.002   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4248)
  covalent geometry    : angle       0.66807 ( 5798)
  SS BOND              : bond        0.00173 (    7)
  SS BOND              : angle       1.12230 (   14)
  hydrogen bonds       : bond        0.03758 (  260)
  hydrogen bonds       : angle       4.44073 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7217 (mp0) cc_final: 0.6774 (mp0)
REVERT: A  233 PHE cc_start: 0.6003 (t80) cc_final: 0.5741 (t80)
REVERT: A  318 ILE cc_start: 0.8525 (mp) cc_final: 0.8159 (mt)
REVERT: A  351 LYS cc_start: 0.8527 (tppt) cc_final: 0.8277 (tptt)
REVERT: A  538 MET cc_start: 0.8538 (mmm) cc_final: 0.8313 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0607
  time to fit residues: 7.0160
Evaluate side-chains
  69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0040
   chunk 34 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4035 r_free = 0.4035 target = 0.182613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.161751 restraints weight = 6990.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.164880 restraints weight = 4447.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.166974 restraints weight = 3109.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.168511 restraints weight = 2355.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.169375 restraints weight = 1915.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4255  Z= 0.133
  Angle     :  0.674   6.577   5812  Z= 0.322
  Chirality :  0.045   0.164    697
  Planarity :  0.004   0.035    696
  Dihedral  :  5.485  39.429    801
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  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:  1.19 (0.40), residues: 516
  helix:  1.59 (0.30), residues: 327
  sheet:  None (None), residues: 0
  loop : -0.60 (0.52), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 627 
 TYR   0.011   0.001   TYR A 597 
 PHE   0.028   0.001   PHE A 551 
 TRP   0.006   0.001   TRP A 583 
 HIS   0.002   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4248)
  covalent geometry    : angle       0.67273 ( 5798)
  SS BOND              : bond        0.00133 (    7)
  SS BOND              : angle       0.97351 (   14)
  hydrogen bonds       : bond        0.03827 (  260)
  hydrogen bonds       : angle       4.52169 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7192 (mp0) cc_final: 0.6751 (mp0)
REVERT: A  318 ILE cc_start: 0.8498 (mp) cc_final: 0.8174 (mt)
REVERT: A  324 MET cc_start: 0.5782 (mtt) cc_final: 0.5395 (mtt)
REVERT: A  351 LYS cc_start: 0.8514 (tppt) cc_final: 0.8290 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0634
  time to fit residues: 7.3514
Evaluate side-chains
  75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4041 r_free = 0.4041 target = 0.183174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.161891 restraints weight = 6804.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.164795 restraints weight = 4391.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166864 restraints weight = 3108.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.168161 restraints weight = 2383.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.169238 restraints weight = 1961.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4255  Z= 0.135
  Angle     :  0.700  10.361   5812  Z= 0.332
  Chirality :  0.045   0.260    697
  Planarity :  0.005   0.040    696
  Dihedral  :  5.544  39.168    801
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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:  1.18 (0.40), residues: 516
  helix:  1.58 (0.30), residues: 327
  sheet:  None (None), residues: 0
  loop : -0.60 (0.52), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 582 
 TYR   0.016   0.002   TYR A 606 
 PHE   0.019   0.001   PHE A 551 
 TRP   0.017   0.001   TRP A 583 
 HIS   0.002   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4248)
  covalent geometry    : angle       0.69913 ( 5798)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       1.11988 (   14)
  hydrogen bonds       : bond        0.03843 (  260)
  hydrogen bonds       : angle       4.51483 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7221 (mp0) cc_final: 0.6787 (mp0)
REVERT: A  318 ILE cc_start: 0.8393 (mp) cc_final: 0.8006 (mt)
REVERT: A  351 LYS cc_start: 0.8440 (tppt) cc_final: 0.8182 (tptt)
REVERT: A  538 MET cc_start: 0.8437 (mmt) cc_final: 0.8128 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0638
  time to fit residues: 7.0368
Evaluate side-chains
  72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0070
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4063 r_free = 0.4063 target = 0.185229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.163793 restraints weight = 6886.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.166850 restraints weight = 4494.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.168706 restraints weight = 3175.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.170317 restraints weight = 2456.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.171394 restraints weight = 2010.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4255  Z= 0.129
  Angle     :  0.689   9.075   5812  Z= 0.325
  Chirality :  0.044   0.235    697
  Planarity :  0.004   0.040    696
  Dihedral  :  5.446  38.821    801
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.28 (0.40), residues: 516
  helix:  1.63 (0.30), residues: 327
  sheet:  None (None), residues: 0
  loop : -0.49 (0.52), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 582 
 TYR   0.015   0.001   TYR A 606 
 PHE   0.017   0.001   PHE A 551 
 TRP   0.008   0.001   TRP A 583 
 HIS   0.003   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4248)
  covalent geometry    : angle       0.68853 ( 5798)
  SS BOND              : bond        0.00193 (    7)
  SS BOND              : angle       0.95312 (   14)
  hydrogen bonds       : bond        0.03711 (  260)
  hydrogen bonds       : angle       4.49705 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7171 (mp0) cc_final: 0.6760 (mp0)
REVERT: A  318 ILE cc_start: 0.8344 (mp) cc_final: 0.7971 (mt)
REVERT: A  351 LYS cc_start: 0.8488 (tppt) cc_final: 0.8216 (tptt)
REVERT: A  538 MET cc_start: 0.8408 (mmt) cc_final: 0.8107 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0669
  time to fit residues: 7.7992
Evaluate side-chains
  74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4062 r_free = 0.4062 target = 0.185306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.163904 restraints weight = 6764.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.166847 restraints weight = 4401.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.168957 restraints weight = 3155.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.170476 restraints weight = 2405.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.171358 restraints weight = 1960.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4255  Z= 0.132
  Angle     :  0.696   8.824   5812  Z= 0.330
  Chirality :  0.045   0.225    697
  Planarity :  0.004   0.041    696
  Dihedral  :  5.473  38.794    801
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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:  1.26 (0.40), residues: 516
  helix:  1.64 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.50 (0.51), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 582 
 TYR   0.015   0.001   TYR A 606 
 PHE   0.016   0.001   PHE A 551 
 TRP   0.006   0.001   TRP A 257 
 HIS   0.003   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4248)
  covalent geometry    : angle       0.69547 ( 5798)
  SS BOND              : bond        0.00164 (    7)
  SS BOND              : angle       0.86276 (   14)
  hydrogen bonds       : bond        0.03732 (  260)
  hydrogen bonds       : angle       4.51398 (  771)

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.7176 (mp0) cc_final: 0.6737 (mp0)
REVERT: A  318 ILE cc_start: 0.8354 (mp) cc_final: 0.7909 (mp)
REVERT: A  351 LYS cc_start: 0.8510 (tppt) cc_final: 0.8138 (tptt)
REVERT: A  538 MET cc_start: 0.8367 (mmt) cc_final: 0.8097 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0642
  time to fit residues: 7.2217
Evaluate side-chains
  70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0060
   chunk 39 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 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 = 0.4069 r_free = 0.4069 target = 0.185894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.164357 restraints weight = 6819.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.167392 restraints weight = 4424.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.169513 restraints weight = 3141.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.171014 restraints weight = 2402.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.171894 restraints weight = 1964.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4255  Z= 0.130
  Angle     :  0.691   8.324   5812  Z= 0.327
  Chirality :  0.044   0.218    697
  Planarity :  0.004   0.041    696
  Dihedral  :  5.422  38.511    801
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.27 (0.40), residues: 516
  helix:  1.68 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.54 (0.51), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 582 
 TYR   0.011   0.001   TYR A 597 
 PHE   0.016   0.001   PHE A 551 
 TRP   0.007   0.001   TRP A 258 
 HIS   0.003   0.000   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4248)
  covalent geometry    : angle       0.69019 ( 5798)
  SS BOND              : bond        0.00132 (    7)
  SS BOND              : angle       0.93851 (   14)
  hydrogen bonds       : bond        0.03741 (  260)
  hydrogen bonds       : angle       4.50157 (  771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 865.99 seconds
wall clock time: 15 minutes 39.18 seconds (939.18 seconds total)