Starting phenix.real_space_refine
on Tue Mar  3 10:50:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b6e_12053/03_2026/7b6e_12053.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.003
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      13      5.16       5
     C    1406      2.51       5
     N     389      2.21       5
     O     397      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2205
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2205
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 4, 'TRANS': 264}
          Chain breaks: 1
  Time building chain proxies: 0.55, per 1000 atoms: 0.25
  Number of scatterers: 2205
  At special positions: 0
  Unit cell: (63.648, 73.632, 92.352, 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      13     16.00
     O     397      8.00
     N     389      7.00
     C    1406      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: 0.19
  Conformation dependent library (CDL) restraints added in 83.5 milliseconds
  

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  522

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      86.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 355 through 384
      removed outlier: 4.194A  pdb=" N   HIS A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      Proline residue:  A 371  - end of helix
    Processing helix  chain 'A' and resid 425 through 438
      removed outlier: 4.158A  pdb=" N   PHE A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 456
    Processing helix  chain 'A' and resid 461 through 477
    Processing helix  chain 'A' and resid 483 through 500
      removed outlier: 3.762A  pdb=" N   THR A 498 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 519
      removed outlier: 4.176A  pdb=" N   ALA A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 535
      removed outlier: 3.905A  pdb=" N   ASN A 535 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 557
      removed outlier: 3.726A  pdb=" N   THR A 556 " --> pdb=" O   CYS A 552 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   GLN A 557 " --> pdb=" O   PHE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 579
      removed outlier: 4.874A  pdb=" N   ARG A 574 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 598
      removed outlier: 3.665A  pdb=" N   ARG A 598 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 614
      removed outlier: 4.015A  pdb=" N   GLU A 604 " --> pdb=" O   TRP A 600 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   HIS A 606 " --> pdb=" O   LEU A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 632
      removed outlier: 4.487A  pdb=" N   ALA A 624 " --> pdb=" O   GLN A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 661

    165 hydrogen bonds defined for protein.
    495 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: 0.20

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 691
        1.34 -     1.46: 378
        1.46 -     1.57: 1162
        1.57 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 2252
  Sorted by residual:
  bond pdb=" CB  PRO A 559 "
       pdb=" CG  PRO A 559 "
    ideal  model  delta    sigma   weight residual
    1.492  1.555 -0.063 5.00e-02 4.00e+02 1.59e+00
  bond pdb=" CG  PRO A 559 "
       pdb=" CD  PRO A 559 "
    ideal  model  delta    sigma   weight residual
    1.503  1.542 -0.039 3.40e-02 8.65e+02 1.32e+00
  bond pdb=" CB  PHE A 436 "
       pdb=" CG  PHE A 436 "
    ideal  model  delta    sigma   weight residual
    1.502  1.476  0.026 2.30e-02 1.89e+03 1.30e+00
  bond pdb=" N   TRP A 600 "
       pdb=" CA  TRP A 600 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.20e+00
  bond pdb=" CG  LEU A 468 "
       pdb=" CD2 LEU A 468 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.14e+00
  ... (remaining 2247 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 2967
        2.79 -     5.59: 63
        5.59 -     8.38: 3
        8.38 -    11.17: 3
       11.17 -    13.96: 1
  Bond angle restraints: 3037
  Sorted by residual:
  angle pdb=" CA  PRO A 559 "
        pdb=" N   PRO A 559 "
        pdb=" CD  PRO A 559 "
      ideal   model   delta    sigma   weight residual
     112.00  102.11    9.89 1.40e+00 5.10e-01 4.99e+01
  angle pdb=" C   LEU A 434 "
        pdb=" N   TYR A 435 "
        pdb=" CA  TYR A 435 "
      ideal   model   delta    sigma   weight residual
     121.58  113.58    8.00 1.95e+00 2.63e-01 1.68e+01
  angle pdb=" CA  LEU A 468 "
        pdb=" CB  LEU A 468 "
        pdb=" CG  LEU A 468 "
      ideal   model   delta    sigma   weight residual
     116.30  130.26  -13.96 3.50e+00 8.16e-02 1.59e+01
  angle pdb=" CA  ARG A 508 "
        pdb=" CB  ARG A 508 "
        pdb=" CG  ARG A 508 "
      ideal   model   delta    sigma   weight residual
     114.10  122.05   -7.95 2.00e+00 2.50e-01 1.58e+01
  angle pdb=" C   ALA A 467 "
        pdb=" N   LEU A 468 "
        pdb=" CA  LEU A 468 "
      ideal   model   delta    sigma   weight residual
     120.31  115.02    5.29 1.52e+00 4.33e-01 1.21e+01
  ... (remaining 3032 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.16: 1143
       15.16 -    30.32: 169
       30.32 -    45.48: 35
       45.48 -    60.64: 2
       60.64 -    75.79: 4
  Dihedral angle restraints: 1353
    sinusoidal: 544
      harmonic: 809
  Sorted by residual:
  dihedral pdb=" CA  ARG A 598 "
           pdb=" C   ARG A 598 "
           pdb=" N   GLU A 599 "
           pdb=" CA  GLU A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.66  -34.34     0      5.00e+00 4.00e-02 4.72e+01
  dihedral pdb=" CA  SER A 538 "
           pdb=" C   SER A 538 "
           pdb=" N   ASP A 539 "
           pdb=" CA  ASP A 539 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.61   25.39     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  GLN A 482 "
           pdb=" C   GLN A 482 "
           pdb=" N   ARG A 483 "
           pdb=" CA  ARG A 483 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 1350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 199
       0.041 -    0.082: 93
       0.082 -    0.123: 23
       0.123 -    0.165: 6
       0.165 -    0.206: 5
  Chirality restraints: 326
  Sorted by residual:
  chirality pdb=" CA  GLN A 529 "
            pdb=" N   GLN A 529 "
            pdb=" C   GLN A 529 "
            pdb=" CB  GLN A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ARG A 508 "
            pdb=" N   ARG A 508 "
            pdb=" C   ARG A 508 "
            pdb=" CB  ARG A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  GLU A 469 "
            pdb=" N   GLU A 469 "
            pdb=" C   GLU A 469 "
            pdb=" CB  GLU A 469 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.21e-01
  ... (remaining 323 not shown)

  Planarity restraints: 388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 558 "    0.075 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO A 559 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO A 559 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 559 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 547 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.32e+00
        pdb=" CD  GLU A 547 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 547 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 547 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 508 "   -0.039 9.50e-02 1.11e+02   2.36e-02 3.33e+00
        pdb=" NE  ARG A 508 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 508 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 508 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 508 "    0.009 2.00e-02 2.50e+03
  ... (remaining 385 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 90
        2.68 -     3.24: 2676
        3.24 -     3.79: 3824
        3.79 -     4.35: 5131
        4.35 -     4.90: 7212
  Nonbonded interactions: 18933
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 471 "
            pdb=" OG  SER A 474 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OE1 GLN A 482 "
            pdb=" NZ  LYS A 484 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" O   CYS A 516 "
            pdb=" OG1 THR A 519 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   GLU A 382 "
            pdb=" OG1 THR A 385 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   ALA A 612 "
            pdb=" N   TYR A 616 "
     model   vdw
     2.203 3.120
  ... (remaining 18928 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:             3.880
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     3.790
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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      :  0.005   0.063   2252  Z= 0.239
  Angle     :  1.026  13.963   3037  Z= 0.575
  Chirality :  0.053   0.206    326
  Planarity :  0.007   0.108    388
  Dihedral  : 15.044  75.794    831
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 36.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.94 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

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 are not related in a simple way.
  whole: -3.88 (0.43), residues: 265
  helix: -2.02 (0.29), residues: 225
  sheet:  None (None), residues: 0
  loop : -4.52 (0.69), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.002   ARG A 508 
 TYR   0.026   0.002   TYR A 435 
 PHE   0.015   0.003   PHE A 628 
 TRP   0.009   0.002   TRP A 600 
 HIS   0.007   0.002   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 2252)
  covalent geometry    : angle       1.02580 ( 3037)
  hydrogen bonds       : bond        0.13536 (  165)
  hydrogen bonds       : angle       7.93452 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  477 MET cc_start: 0.8355 (ptp) cc_final: 0.7802 (pmm)
REVERT: A  484 LYS cc_start: 0.9700 (ptpp) cc_final: 0.9389 (pttp)
REVERT: A  606 HIS cc_start: 0.8591 (m-70) cc_final: 0.8296 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0789
  time to fit residues: 2.7516
Evaluate side-chains
  25 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.063983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.054160 restraints weight = 18921.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.055704 restraints weight = 12890.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.056803 restraints weight = 9391.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.057636 restraints weight = 7243.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.058202 restraints weight = 5812.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2252  Z= 0.188
  Angle     :  0.866  11.616   3037  Z= 0.458
  Chirality :  0.048   0.177    326
  Planarity :  0.005   0.040    388
  Dihedral  :  6.899  25.692    306
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 22.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.33 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole: -2.68 (0.46), residues: 265
  helix: -1.13 (0.31), residues: 221
  sheet:  None (None), residues: 0
  loop : -4.35 (0.69), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 508 
 TYR   0.023   0.002   TYR A 435 
 PHE   0.027   0.003   PHE A 628 
 TRP   0.008   0.001   TRP A 600 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 2252)
  covalent geometry    : angle       0.86573 ( 3037)
  hydrogen bonds       : bond        0.05962 (  165)
  hydrogen bonds       : angle       6.30722 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 LEU cc_start: 0.9406 (mm) cc_final: 0.9011 (tp)
REVERT: A  552 CYS cc_start: 0.9272 (m) cc_final: 0.8867 (m)
REVERT: A  606 HIS cc_start: 0.8549 (m-70) cc_final: 0.8272 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0697
  time to fit residues: 2.8510
Evaluate side-chains
  26 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   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 580 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 = 0.3802 r_free = 0.3802 target = 0.064400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.054673 restraints weight = 19470.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.056063 restraints weight = 13413.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.057121 restraints weight = 9910.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.057926 restraints weight = 7700.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.058542 restraints weight = 6215.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2252  Z= 0.174
  Angle     :  0.860  11.028   3037  Z= 0.452
  Chirality :  0.046   0.186    326
  Planarity :  0.004   0.038    388
  Dihedral  :  6.661  26.217    306
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 22.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.47), residues: 265
  helix: -0.78 (0.32), residues: 221
  sheet:  None (None), residues: 0
  loop : -4.17 (0.71), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 508 
 TYR   0.026   0.002   TYR A 488 
 PHE   0.011   0.002   PHE A 553 
 TRP   0.007   0.001   TRP A 600 
 HIS   0.003   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2252)
  covalent geometry    : angle       0.86026 ( 3037)
  hydrogen bonds       : bond        0.05783 (  165)
  hydrogen bonds       : angle       6.15504 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8710 (mmt180) cc_final: 0.8504 (mmt180)
REVERT: A  484 LYS cc_start: 0.9366 (pttm) cc_final: 0.8919 (pttp)
REVERT: A  508 ARG cc_start: 0.8716 (ptt-90) cc_final: 0.8365 (ptp-170)
REVERT: A  533 MET cc_start: 0.7315 (ttt) cc_final: 0.6987 (ttt)
REVERT: A  552 CYS cc_start: 0.9111 (m) cc_final: 0.8760 (m)
REVERT: A  606 HIS cc_start: 0.8510 (m-70) cc_final: 0.8176 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0895
  time to fit residues: 3.4435
Evaluate side-chains
  27 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 375 HIS
** A 580 GLN ** 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 = 0.3785 r_free = 0.3785 target = 0.063758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.054140 restraints weight = 19729.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.055498 restraints weight = 13694.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.056488 restraints weight = 10226.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.057154 restraints weight = 8043.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.057786 restraints weight = 6669.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2252  Z= 0.178
  Angle     :  0.897  13.803   3037  Z= 0.452
  Chirality :  0.046   0.185    326
  Planarity :  0.004   0.034    388
  Dihedral  :  6.560  24.763    306
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  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 are not related in a simple way.
  whole: -1.98 (0.48), residues: 265
  helix: -0.63 (0.33), residues: 221
  sheet:  None (None), residues: 0
  loop : -4.28 (0.68), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 508 
 TYR   0.031   0.002   TYR A 488 
 PHE   0.014   0.002   PHE A 553 
 TRP   0.004   0.001   TRP A 600 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2252)
  covalent geometry    : angle       0.89738 ( 3037)
  hydrogen bonds       : bond        0.05490 (  165)
  hydrogen bonds       : angle       6.03504 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  483 ARG cc_start: 0.8789 (mmt180) cc_final: 0.8398 (mmt180)
REVERT: A  484 LYS cc_start: 0.9359 (pttm) cc_final: 0.8963 (pttp)
REVERT: A  508 ARG cc_start: 0.8805 (ptt-90) cc_final: 0.8303 (ptp-170)
REVERT: A  547 GLU cc_start: 0.8944 (tt0) cc_final: 0.8702 (tt0)
REVERT: A  606 HIS cc_start: 0.8457 (m-70) cc_final: 0.8138 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0959
  time to fit residues: 3.5592
Evaluate side-chains
  26 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0370
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 16 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0970
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.076809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.066167 restraints weight = 20920.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.067651 restraints weight = 13457.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.068715 restraints weight = 9509.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.069459 restraints weight = 7129.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.070008 restraints weight = 5652.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2252  Z= 0.172
  Angle     :  0.900  13.932   3037  Z= 0.455
  Chirality :  0.046   0.178    326
  Planarity :  0.004   0.032    388
  Dihedral  :  6.392  24.164    306
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 23.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  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 are not related in a simple way.
  whole: -1.81 (0.48), residues: 265
  helix: -0.49 (0.33), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.22 (0.63), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 508 
 TYR   0.029   0.002   TYR A 488 
 PHE   0.010   0.002   PHE A 553 
 TRP   0.006   0.001   TRP A 600 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2252)
  covalent geometry    : angle       0.90041 ( 3037)
  hydrogen bonds       : bond        0.05362 (  165)
  hydrogen bonds       : angle       5.99090 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  470 MET cc_start: 0.8107 (ptt) cc_final: 0.7697 (ptp)
REVERT: A  484 LYS cc_start: 0.9296 (pttm) cc_final: 0.9053 (pptt)
REVERT: A  491 ASP cc_start: 0.9344 (m-30) cc_final: 0.9061 (t0)
REVERT: A  501 LYS cc_start: 0.8635 (mmpt) cc_final: 0.8413 (mmmt)
REVERT: A  508 ARG cc_start: 0.8805 (ptt-90) cc_final: 0.8254 (ptp-170)
REVERT: A  547 GLU cc_start: 0.8813 (tt0) cc_final: 0.8601 (tt0)
REVERT: A  606 HIS cc_start: 0.8461 (m-70) cc_final: 0.8174 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0971
  time to fit residues: 3.5217
Evaluate side-chains
  29 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.063481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.054156 restraints weight = 19799.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.055508 restraints weight = 13695.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.056523 restraints weight = 10207.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.057257 restraints weight = 8006.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.057845 restraints weight = 6527.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2252  Z= 0.177
  Angle     :  0.864  12.993   3037  Z= 0.433
  Chirality :  0.045   0.168    326
  Planarity :  0.004   0.030    388
  Dihedral  :  6.356  24.678    306
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 26.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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 are not related in a simple way.
  whole: -1.89 (0.47), residues: 265
  helix: -0.53 (0.33), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.30 (0.61), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 508 
 TYR   0.026   0.002   TYR A 486 
 PHE   0.014   0.002   PHE A 553 
 TRP   0.003   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2252)
  covalent geometry    : angle       0.86380 ( 3037)
  hydrogen bonds       : bond        0.05328 (  165)
  hydrogen bonds       : angle       5.91763 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.049 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8894 (mmt180) cc_final: 0.8312 (mmt180)
REVERT: A  484 LYS cc_start: 0.9265 (pttm) cc_final: 0.8875 (pptt)
REVERT: A  501 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8371 (mmmt)
REVERT: A  547 GLU cc_start: 0.8857 (tt0) cc_final: 0.8599 (tt0)
REVERT: A  606 HIS cc_start: 0.8553 (m-70) cc_final: 0.8266 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0860
  time to fit residues: 3.4272
Evaluate side-chains
  29 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.076232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.065625 restraints weight = 20517.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.067166 restraints weight = 13265.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.068189 restraints weight = 9284.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.068937 restraints weight = 6989.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.069499 restraints weight = 5540.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2252  Z= 0.169
  Angle     :  0.907  15.207   3037  Z= 0.450
  Chirality :  0.046   0.182    326
  Planarity :  0.004   0.030    388
  Dihedral  :  6.291  23.532    306
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 22.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  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 are not related in a simple way.
  whole: -1.62 (0.48), residues: 265
  helix: -0.33 (0.34), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.27 (0.61), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 508 
 TYR   0.046   0.002   TYR A 488 
 PHE   0.011   0.002   PHE A 628 
 TRP   0.005   0.001   TRP A 600 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2252)
  covalent geometry    : angle       0.90703 ( 3037)
  hydrogen bonds       : bond        0.05200 (  165)
  hydrogen bonds       : angle       5.79241 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8741 (mmt180) cc_final: 0.8306 (mmt180)
REVERT: A  491 ASP cc_start: 0.9314 (m-30) cc_final: 0.9052 (t0)
REVERT: A  501 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8350 (mmmt)
REVERT: A  606 HIS cc_start: 0.8392 (m-70) cc_final: 0.8109 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0828
  time to fit residues: 3.2446
Evaluate side-chains
  28 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.069990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.061085 restraints weight = 20168.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.062563 restraints weight = 12761.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.063574 restraints weight = 8879.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.064295 restraints weight = 6645.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.064802 restraints weight = 5247.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2252  Z= 0.176
  Angle     :  0.894  14.826   3037  Z= 0.445
  Chirality :  0.045   0.176    326
  Planarity :  0.004   0.028    388
  Dihedral  :  6.269  23.433    306
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 25.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  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 are not related in a simple way.
  whole: -1.60 (0.48), residues: 265
  helix: -0.31 (0.34), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.35 (0.60), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 633 
 TYR   0.025   0.002   TYR A 488 
 PHE   0.013   0.002   PHE A 553 
 TRP   0.003   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 2252)
  covalent geometry    : angle       0.89407 ( 3037)
  hydrogen bonds       : bond        0.05190 (  165)
  hydrogen bonds       : angle       5.76557 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8662 (mmt180) cc_final: 0.8172 (mmt180)
REVERT: A  484 LYS cc_start: 0.9394 (pttm) cc_final: 0.9101 (pptt)
REVERT: A  501 LYS cc_start: 0.8519 (mmpt) cc_final: 0.8265 (mmmt)
REVERT: A  606 HIS cc_start: 0.8434 (m-70) cc_final: 0.8144 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0898
  time to fit residues: 3.4398
Evaluate side-chains
  28 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.064965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.055408 restraints weight = 19594.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.056886 restraints weight = 13498.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.057921 restraints weight = 9954.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.058690 restraints weight = 7735.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.059307 restraints weight = 6249.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2252  Z= 0.176
  Angle     :  0.929  15.528   3037  Z= 0.468
  Chirality :  0.046   0.172    326
  Planarity :  0.004   0.028    388
  Dihedral  :  6.233  24.402    306
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 21.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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 are not related in a simple way.
  whole: -1.60 (0.49), residues: 265
  helix: -0.25 (0.34), residues: 218
  sheet:  None (None), residues: 0
  loop : -4.59 (0.55), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 598 
 TYR   0.020   0.002   TYR A 575 
 PHE   0.012   0.002   PHE A 436 
 TRP   0.005   0.001   TRP A 600 
 HIS   0.004   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2252)
  covalent geometry    : angle       0.92900 ( 3037)
  hydrogen bonds       : bond        0.05140 (  165)
  hydrogen bonds       : angle       5.89345 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8797 (mmt180) cc_final: 0.8302 (mpt180)
REVERT: A  484 LYS cc_start: 0.9374 (pttm) cc_final: 0.8897 (pptt)
REVERT: A  491 ASP cc_start: 0.9357 (m-30) cc_final: 0.9106 (t0)
REVERT: A  501 LYS cc_start: 0.8633 (mmpt) cc_final: 0.8392 (mmmt)
REVERT: A  547 GLU cc_start: 0.8911 (tt0) cc_final: 0.8704 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1010
  time to fit residues: 3.7100
Evaluate side-chains
  32 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 15 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.070804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.061625 restraints weight = 20226.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.063139 restraints weight = 12887.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.064166 restraints weight = 9056.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.064915 restraints weight = 6841.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.065430 restraints weight = 5426.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.4588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2252  Z= 0.175
  Angle     :  0.926  15.545   3037  Z= 0.465
  Chirality :  0.046   0.179    326
  Planarity :  0.004   0.028    388
  Dihedral  :  6.209  22.873    306
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 20.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.48), residues: 265
  helix: -0.21 (0.34), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.48 (0.58), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 633 
 TYR   0.031   0.002   TYR A 488 
 PHE   0.010   0.002   PHE A 553 
 TRP   0.005   0.001   TRP A 600 
 HIS   0.005   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2252)
  covalent geometry    : angle       0.92594 ( 3037)
  hydrogen bonds       : bond        0.05183 (  165)
  hydrogen bonds       : angle       5.76182 (  495)

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

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

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  530 Ramachandran restraints generated.
    265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 ARG cc_start: 0.8686 (mmt180) cc_final: 0.8136 (mmt-90)
REVERT: A  491 ASP cc_start: 0.9267 (m-30) cc_final: 0.9023 (t0)
REVERT: A  501 LYS cc_start: 0.8491 (mmpt) cc_final: 0.8273 (mmmt)
REVERT: A  533 MET cc_start: 0.7288 (ttt) cc_final: 0.7075 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0753
  time to fit residues: 2.9127
Evaluate side-chains
  30 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0970
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 606 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.076413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.065843 restraints weight = 20455.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.067358 restraints weight = 13194.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.068358 restraints weight = 9312.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.069082 restraints weight = 7061.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.069611 restraints weight = 5635.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2252  Z= 0.180
  Angle     :  0.951  15.821   3037  Z= 0.472
  Chirality :  0.046   0.164    326
  Planarity :  0.004   0.027    388
  Dihedral  :  6.254  22.368    306
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 22.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  0.88 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.49), residues: 265
  helix: -0.30 (0.34), residues: 219
  sheet:  None (None), residues: 0
  loop : -4.67 (0.56), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 574 
 TYR   0.032   0.002   TYR A 575 
 PHE   0.010   0.002   PHE A 628 
 TRP   0.005   0.001   TRP A 461 
 HIS   0.010   0.002   HIS A 606 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 2252)
  covalent geometry    : angle       0.95147 ( 3037)
  hydrogen bonds       : bond        0.05118 (  165)
  hydrogen bonds       : angle       5.76932 (  495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 638.39 seconds
wall clock time: 11 minutes 36.06 seconds (696.06 seconds total)