Starting phenix.real_space_refine on Mon Apr 6 16:22:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.map" model { file = "/net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nf7_49347/04_2026/9nf7_49347.cif" } resolution = 2.44 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= 0.058 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 6594 2.51 5 N 1680 2.21 5 O 1770 1.98 5 H 9578 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19638 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 9813 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 36, 'TRANS': 614} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 9813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 9813 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 36, 'TRANS': 614} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.82, per 1000 atoms: 0.19 Number of scatterers: 19638 At special positions: 0 Unit cell: (113.827, 99.0869, 114.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 1770 8.00 N 1680 7.00 C 6594 6.00 H 9578 1.00 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: 1.92 Conformation dependent library (CDL) restraints added in 576.0 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 66.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 89 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.971A pdb=" N GLY A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 121 through 139 Processing helix chain 'A' and resid 140 through 143 removed outlier: 4.580A pdb=" N TRP A 143 " --> pdb=" O GLY A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.645A pdb=" N VAL A 172 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 201 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 228 through 254 removed outlier: 3.885A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.684A pdb=" N MET A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 326 through 349 Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.768A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 467 through 488 Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 89 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.971A pdb=" N GLY B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 121 through 139 Processing helix chain 'B' and resid 140 through 143 removed outlier: 4.580A pdb=" N TRP B 143 " --> pdb=" O GLY B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.635A pdb=" N VAL B 172 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 Proline residue: B 197 - end of helix Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 228 through 254 removed outlier: 3.884A pdb=" N PHE B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.683A pdb=" N MET B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 326 through 349 Processing helix chain 'B' and resid 354 through 370 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.768A pdb=" N VAL B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 467 through 488 Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 617 through 636 Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 676 through 680 Processing helix chain 'B' and resid 747 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 514 removed outlier: 4.534A pdb=" N ILE A 537 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N LYS A 497 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.763A pdb=" N VAL A 535 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 536 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASP A 609 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE A 538 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS A 745 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 643 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 514 removed outlier: 4.534A pdb=" N ILE B 537 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS B 497 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.760A pdb=" N VAL B 535 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE B 536 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP B 609 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE B 538 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N HIS B 745 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 643 " --> pdb=" O HIS B 745 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1782 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: 4.76 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9572 1.03 - 1.23: 9 1.23 - 1.42: 4317 1.42 - 1.62: 5974 1.62 - 1.81: 22 Bond restraints: 19894 Sorted by residual: bond pdb=" CG1 ILE A 472 " pdb=" CD1 ILE A 472 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB ILE B 368 " pdb=" CG2 ILE B 368 " ideal model delta sigma weight residual 1.521 1.567 -0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.98e+00 bond pdb=" CB ILE A 368 " pdb=" CG2 ILE A 368 " ideal model delta sigma weight residual 1.521 1.567 -0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB ILE A 53 " pdb=" CG2 ILE A 53 " ideal model delta sigma weight residual 1.521 1.562 -0.041 3.30e-02 9.18e+02 1.55e+00 ... (remaining 19889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 34693 1.75 - 3.51: 870 3.51 - 5.26: 143 5.26 - 7.01: 14 7.01 - 8.77: 4 Bond angle restraints: 35724 Sorted by residual: angle pdb=" CA TYR A 254 " pdb=" CB TYR A 254 " pdb=" CG TYR A 254 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" CA TYR B 254 " pdb=" CB TYR B 254 " pdb=" CG TYR B 254 " ideal model delta sigma weight residual 113.90 120.16 -6.26 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C SER A 543 " pdb=" N PHE A 544 " pdb=" CA PHE A 544 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.60e+00 angle pdb=" O1 SO4 B 801 " pdb=" S SO4 B 801 " pdb=" O2 SO4 B 801 " ideal model delta sigma weight residual 109.49 100.72 8.77 3.00e+00 1.11e-01 8.54e+00 angle pdb=" O1 SO4 A 801 " pdb=" S SO4 A 801 " pdb=" O2 SO4 A 801 " ideal model delta sigma weight residual 109.49 100.73 8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 35719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 8336 17.61 - 35.22: 768 35.22 - 52.83: 240 52.83 - 70.43: 100 70.43 - 88.04: 10 Dihedral angle restraints: 9454 sinusoidal: 4966 harmonic: 4488 Sorted by residual: dihedral pdb=" CA VAL A 283 " pdb=" C VAL A 283 " pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA VAL B 283 " pdb=" C VAL B 283 " pdb=" N VAL B 284 " pdb=" CA VAL B 284 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU B 206 " pdb=" C LEU B 206 " pdb=" N ASP B 207 " pdb=" CA ASP B 207 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 9451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 999 0.032 - 0.064: 437 0.064 - 0.096: 134 0.096 - 0.128: 67 0.128 - 0.160: 11 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CA VAL B 303 " pdb=" N VAL B 303 " pdb=" C VAL B 303 " pdb=" CB VAL B 303 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL A 303 " pdb=" N VAL A 303 " pdb=" C VAL A 303 " pdb=" CB VAL A 303 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE A 472 " pdb=" N ILE A 472 " pdb=" C ILE A 472 " pdb=" CB ILE A 472 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1645 not shown) Planarity restraints: 2902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 285 " 0.168 9.50e-02 1.11e+02 5.68e-02 5.14e+00 pdb=" NE ARG A 285 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 285 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 285 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 285 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 285 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 285 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 285 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 285 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 285 " -0.166 9.50e-02 1.11e+02 5.62e-02 4.97e+00 pdb=" NE ARG B 285 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 285 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 285 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 285 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 285 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 285 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG B 285 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 285 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 50 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 51 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.028 5.00e-02 4.00e+02 ... (remaining 2899 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 3245 2.29 - 2.87: 44395 2.87 - 3.45: 52733 3.45 - 4.02: 72623 4.02 - 4.60: 109634 Nonbonded interactions: 282630 Sorted by model distance: nonbonded pdb=" OG SER B 466 " pdb="HD22 ASN B 470 " model vdw 1.713 2.450 nonbonded pdb=" OG SER A 466 " pdb="HD22 ASN A 470 " model vdw 1.714 2.450 nonbonded pdb=" H ARG A 565 " pdb=" O PRO A 601 " model vdw 1.718 2.450 nonbonded pdb=" H ARG B 565 " pdb=" O PRO B 601 " model vdw 1.719 2.450 nonbonded pdb=" O PHE A 536 " pdb=" H VAL A 607 " model vdw 1.726 2.450 ... (remaining 282625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 0.056 10316 Z= 0.181 Angle : 0.730 8.767 14076 Z= 0.372 Chirality : 0.043 0.160 1648 Planarity : 0.007 0.077 1760 Dihedral : 14.883 88.042 3594 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.19 % Allowed : 18.10 % Favored : 81.72 % 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: -0.30 (0.22), residues: 1282 helix: 0.49 (0.17), residues: 770 sheet: 0.05 (0.71), residues: 60 loop : -1.35 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 285 TYR 0.030 0.002 TYR B 134 PHE 0.025 0.002 PHE A 183 TRP 0.019 0.002 TRP B 281 HIS 0.013 0.002 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00451 (10316) covalent geometry : angle 0.73035 (14076) hydrogen bonds : bond 0.20613 ( 616) hydrogen bonds : angle 7.11237 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.471 Fit side-chains REVERT: A 58 ASN cc_start: 0.7674 (m-40) cc_final: 0.7312 (p0) REVERT: A 257 ARG cc_start: 0.6385 (mtp85) cc_final: 0.5878 (mmm-85) REVERT: A 509 ARG cc_start: 0.6598 (mmt-90) cc_final: 0.5866 (mpp-170) REVERT: A 578 ARG cc_start: 0.7314 (ttp-110) cc_final: 0.6343 (ttp80) REVERT: A 629 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7308 (mmtt) REVERT: A 650 TRP cc_start: 0.6512 (m100) cc_final: 0.5737 (m-10) REVERT: A 682 ASP cc_start: 0.7687 (p0) cc_final: 0.6812 (m-30) REVERT: B 58 ASN cc_start: 0.7678 (m-40) cc_final: 0.7318 (p0) REVERT: B 257 ARG cc_start: 0.6406 (mtp85) cc_final: 0.5893 (mmm-85) REVERT: B 509 ARG cc_start: 0.6612 (mmt-90) cc_final: 0.5860 (mpp-170) REVERT: B 578 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.6341 (ttp80) REVERT: B 629 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7328 (mmtt) REVERT: B 650 TRP cc_start: 0.6504 (m100) cc_final: 0.5568 (m100) REVERT: B 682 ASP cc_start: 0.7701 (p0) cc_final: 0.6801 (m-30) outliers start: 2 outliers final: 2 residues processed: 99 average time/residue: 1.0947 time to fit residues: 117.9481 Evaluate side-chains 102 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain B residue 183 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 441 GLN A 470 ASN A 679 GLN B 326 HIS B 441 GLN B 470 ASN B 679 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135582 restraints weight = 34879.985| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.68 r_work: 0.3590 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10316 Z= 0.152 Angle : 0.551 4.898 14076 Z= 0.301 Chirality : 0.041 0.143 1648 Planarity : 0.006 0.051 1760 Dihedral : 4.985 48.789 1400 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.12 % Allowed : 17.16 % Favored : 81.72 % 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: 0.76 (0.23), residues: 1282 helix: 1.62 (0.18), residues: 778 sheet: -0.08 (0.70), residues: 60 loop : -1.47 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 565 TYR 0.015 0.001 TYR B 375 PHE 0.018 0.002 PHE A 345 TRP 0.011 0.001 TRP B 281 HIS 0.004 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00333 (10316) covalent geometry : angle 0.55098 (14076) hydrogen bonds : bond 0.05784 ( 616) hydrogen bonds : angle 4.79782 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.466 Fit side-chains REVERT: A 58 ASN cc_start: 0.7674 (m-40) cc_final: 0.7320 (p0) REVERT: A 173 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 184 MET cc_start: 0.8722 (mmt) cc_final: 0.8034 (mmt) REVERT: A 257 ARG cc_start: 0.6289 (mtp85) cc_final: 0.5757 (mmm-85) REVERT: A 509 ARG cc_start: 0.6585 (mmt-90) cc_final: 0.5821 (mtm180) REVERT: A 629 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7247 (mmtt) REVERT: A 650 TRP cc_start: 0.6512 (m100) cc_final: 0.5631 (m100) REVERT: A 682 ASP cc_start: 0.7527 (p0) cc_final: 0.6704 (m-30) REVERT: B 58 ASN cc_start: 0.7674 (m-40) cc_final: 0.7315 (p0) REVERT: B 173 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7541 (tp30) REVERT: B 257 ARG cc_start: 0.6285 (mtp85) cc_final: 0.5754 (mmm-85) REVERT: B 509 ARG cc_start: 0.6612 (mmt-90) cc_final: 0.5835 (mtm180) REVERT: B 629 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7252 (mmtt) REVERT: B 650 TRP cc_start: 0.6494 (m100) cc_final: 0.5613 (m100) REVERT: B 682 ASP cc_start: 0.7536 (p0) cc_final: 0.6679 (m-30) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 1.0037 time to fit residues: 113.4458 Evaluate side-chains 101 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 553 ASN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 553 ASN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133315 restraints weight = 34827.680| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.66 r_work: 0.3558 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10316 Z= 0.177 Angle : 0.552 5.391 14076 Z= 0.299 Chirality : 0.041 0.140 1648 Planarity : 0.006 0.058 1760 Dihedral : 5.078 49.508 1400 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.76 % Favored : 95.09 % Rotamer: Outliers : 2.05 % Allowed : 15.86 % Favored : 82.09 % 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: 0.71 (0.24), residues: 1282 helix: 1.67 (0.18), residues: 780 sheet: -0.32 (0.67), residues: 60 loop : -1.66 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.014 0.001 TYR A 375 PHE 0.022 0.002 PHE B 345 TRP 0.008 0.001 TRP B 55 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00411 (10316) covalent geometry : angle 0.55214 (14076) hydrogen bonds : bond 0.05643 ( 616) hydrogen bonds : angle 4.56621 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.405 Fit side-chains REVERT: A 58 ASN cc_start: 0.7654 (m-40) cc_final: 0.7341 (p0) REVERT: A 183 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7856 (t80) REVERT: A 257 ARG cc_start: 0.6445 (mtp85) cc_final: 0.6020 (mmm-85) REVERT: A 509 ARG cc_start: 0.6648 (mmt-90) cc_final: 0.5927 (mtm180) REVERT: A 578 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6393 (ttp80) REVERT: A 629 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7316 (mmtt) REVERT: A 650 TRP cc_start: 0.6560 (m100) cc_final: 0.5691 (m100) REVERT: A 682 ASP cc_start: 0.7627 (p0) cc_final: 0.6791 (m-30) REVERT: B 58 ASN cc_start: 0.7656 (m-40) cc_final: 0.7337 (p0) REVERT: B 173 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7776 (tp30) REVERT: B 183 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 257 ARG cc_start: 0.6481 (mtp85) cc_final: 0.6049 (mmm-85) REVERT: B 509 ARG cc_start: 0.6648 (mmt-90) cc_final: 0.5925 (mtm180) REVERT: B 578 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5627 (ppt170) REVERT: B 629 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7317 (mmtt) REVERT: B 650 TRP cc_start: 0.6520 (m100) cc_final: 0.5656 (m100) REVERT: B 682 ASP cc_start: 0.7603 (p0) cc_final: 0.6755 (m-30) outliers start: 22 outliers final: 12 residues processed: 116 average time/residue: 0.9207 time to fit residues: 117.9009 Evaluate side-chains 112 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132033 restraints weight = 34797.093| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.67 r_work: 0.3527 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10316 Z= 0.196 Angle : 0.566 5.758 14076 Z= 0.307 Chirality : 0.042 0.142 1648 Planarity : 0.007 0.068 1760 Dihedral : 5.200 51.211 1400 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 2.52 % Allowed : 14.37 % Favored : 83.12 % 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: 0.65 (0.24), residues: 1282 helix: 1.62 (0.18), residues: 780 sheet: -0.39 (0.67), residues: 60 loop : -1.67 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 383 TYR 0.015 0.002 TYR B 95 PHE 0.023 0.002 PHE A 345 TRP 0.009 0.001 TRP A 55 HIS 0.006 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00456 (10316) covalent geometry : angle 0.56641 (14076) hydrogen bonds : bond 0.05520 ( 616) hydrogen bonds : angle 4.53458 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7711 (m-40) cc_final: 0.7379 (p0) REVERT: A 183 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 257 ARG cc_start: 0.6620 (mtp85) cc_final: 0.6114 (mmm-85) REVERT: A 578 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6274 (ttp80) REVERT: A 629 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7392 (mmtt) REVERT: A 650 TRP cc_start: 0.6601 (m100) cc_final: 0.5721 (m100) REVERT: A 682 ASP cc_start: 0.7585 (p0) cc_final: 0.6739 (m-30) REVERT: B 58 ASN cc_start: 0.7703 (m-40) cc_final: 0.7365 (p0) REVERT: B 183 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 257 ARG cc_start: 0.6614 (mtp85) cc_final: 0.6089 (mmm-85) REVERT: B 578 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6347 (ttp80) REVERT: B 629 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7387 (mmtt) REVERT: B 650 TRP cc_start: 0.6575 (m100) cc_final: 0.5692 (m100) REVERT: B 682 ASP cc_start: 0.7597 (p0) cc_final: 0.6755 (m-30) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.8912 time to fit residues: 115.2569 Evaluate side-chains 112 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133233 restraints weight = 34624.912| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.63 r_work: 0.3560 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10316 Z= 0.162 Angle : 0.535 4.989 14076 Z= 0.289 Chirality : 0.041 0.137 1648 Planarity : 0.006 0.056 1760 Dihedral : 5.107 52.680 1400 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.68 % Favored : 95.16 % Rotamer: Outliers : 2.99 % Allowed : 14.65 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1282 helix: 1.76 (0.18), residues: 782 sheet: -0.37 (0.66), residues: 60 loop : -1.72 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.013 0.001 TYR B 375 PHE 0.021 0.002 PHE B 345 TRP 0.008 0.001 TRP B 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00373 (10316) covalent geometry : angle 0.53472 (14076) hydrogen bonds : bond 0.05103 ( 616) hydrogen bonds : angle 4.42906 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7653 (m-40) cc_final: 0.7356 (p0) REVERT: A 183 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 257 ARG cc_start: 0.6499 (mtp85) cc_final: 0.5977 (mmm-85) REVERT: A 509 ARG cc_start: 0.6639 (mmt-90) cc_final: 0.5957 (mtm180) REVERT: A 529 GLU cc_start: 0.7138 (pm20) cc_final: 0.6885 (pt0) REVERT: A 578 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6287 (ttp80) REVERT: A 629 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7405 (mmtt) REVERT: A 650 TRP cc_start: 0.6607 (m100) cc_final: 0.5740 (m100) REVERT: A 682 ASP cc_start: 0.7604 (p0) cc_final: 0.6778 (m-30) REVERT: B 58 ASN cc_start: 0.7701 (m-40) cc_final: 0.7366 (p0) REVERT: B 183 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 257 ARG cc_start: 0.6508 (mtp85) cc_final: 0.5986 (mmm-85) REVERT: B 509 ARG cc_start: 0.6625 (mmt-90) cc_final: 0.5944 (mtm180) REVERT: B 529 GLU cc_start: 0.7147 (pm20) cc_final: 0.6891 (pt0) REVERT: B 578 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6302 (ttp80) REVERT: B 629 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7391 (mmtt) REVERT: B 650 TRP cc_start: 0.6573 (m100) cc_final: 0.5706 (m100) REVERT: B 682 ASP cc_start: 0.7563 (p0) cc_final: 0.6738 (m-30) outliers start: 32 outliers final: 23 residues processed: 122 average time/residue: 0.9681 time to fit residues: 129.8030 Evaluate side-chains 120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133056 restraints weight = 34619.473| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.66 r_work: 0.3556 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10316 Z= 0.159 Angle : 0.528 5.157 14076 Z= 0.285 Chirality : 0.041 0.137 1648 Planarity : 0.006 0.056 1760 Dihedral : 5.061 54.206 1400 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.68 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 14.09 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1282 helix: 1.84 (0.18), residues: 784 sheet: -0.42 (0.66), residues: 60 loop : -1.73 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.013 0.001 TYR B 95 PHE 0.021 0.002 PHE B 345 TRP 0.008 0.001 TRP B 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00364 (10316) covalent geometry : angle 0.52790 (14076) hydrogen bonds : bond 0.04969 ( 616) hydrogen bonds : angle 4.37069 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7662 (m-40) cc_final: 0.7347 (p0) REVERT: A 183 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 184 MET cc_start: 0.8752 (mmt) cc_final: 0.8358 (mmt) REVERT: A 209 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7013 (mmm160) REVERT: A 257 ARG cc_start: 0.6472 (mtp85) cc_final: 0.5955 (mmm-85) REVERT: A 529 GLU cc_start: 0.7172 (pm20) cc_final: 0.6941 (pt0) REVERT: A 578 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6427 (ttp80) REVERT: A 629 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7534 (mptm) REVERT: A 650 TRP cc_start: 0.6580 (m100) cc_final: 0.5726 (m100) REVERT: A 682 ASP cc_start: 0.7588 (p0) cc_final: 0.6763 (m-30) REVERT: B 58 ASN cc_start: 0.7670 (m-40) cc_final: 0.7335 (p0) REVERT: B 183 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 184 MET cc_start: 0.8774 (mmt) cc_final: 0.8384 (mmt) REVERT: B 257 ARG cc_start: 0.6507 (mtp85) cc_final: 0.5979 (mmm-85) REVERT: B 529 GLU cc_start: 0.7180 (pm20) cc_final: 0.6946 (pt0) REVERT: B 578 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6364 (ttp80) REVERT: B 629 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7515 (mptm) REVERT: B 650 TRP cc_start: 0.6552 (m100) cc_final: 0.5699 (m100) REVERT: B 682 ASP cc_start: 0.7557 (p0) cc_final: 0.6744 (m-30) outliers start: 34 outliers final: 20 residues processed: 120 average time/residue: 1.0645 time to fit residues: 139.2976 Evaluate side-chains 119 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 441 GLN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 441 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132258 restraints weight = 34785.877| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.67 r_work: 0.3546 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10316 Z= 0.173 Angle : 0.539 5.113 14076 Z= 0.291 Chirality : 0.041 0.139 1648 Planarity : 0.006 0.061 1760 Dihedral : 5.120 55.290 1400 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Rotamer: Outliers : 2.43 % Allowed : 14.37 % Favored : 83.21 % 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: 0.83 (0.24), residues: 1282 helix: 1.83 (0.18), residues: 782 sheet: -0.51 (0.66), residues: 60 loop : -1.74 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.014 0.001 TYR B 95 PHE 0.022 0.002 PHE B 345 TRP 0.008 0.001 TRP A 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00401 (10316) covalent geometry : angle 0.53881 (14076) hydrogen bonds : bond 0.05117 ( 616) hydrogen bonds : angle 4.36767 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7690 (m-40) cc_final: 0.7348 (p0) REVERT: A 183 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 184 MET cc_start: 0.8763 (mmt) cc_final: 0.8456 (mmt) REVERT: A 209 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7368 (mmm160) REVERT: A 257 ARG cc_start: 0.6471 (mtp85) cc_final: 0.5938 (mmm-85) REVERT: A 529 GLU cc_start: 0.7241 (pm20) cc_final: 0.6951 (pt0) REVERT: A 578 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6320 (ttp80) REVERT: A 629 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7542 (mptm) REVERT: A 650 TRP cc_start: 0.6588 (m100) cc_final: 0.5732 (m100) REVERT: A 682 ASP cc_start: 0.7612 (p0) cc_final: 0.6779 (m-30) REVERT: B 58 ASN cc_start: 0.7690 (m-40) cc_final: 0.7335 (p0) REVERT: B 183 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7638 (t80) REVERT: B 184 MET cc_start: 0.8775 (mmt) cc_final: 0.8472 (mmt) REVERT: B 209 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: B 257 ARG cc_start: 0.6503 (mtp85) cc_final: 0.5969 (mmm-85) REVERT: B 529 GLU cc_start: 0.7236 (pm20) cc_final: 0.6953 (pt0) REVERT: B 578 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6336 (ttp80) REVERT: B 629 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7525 (mptm) REVERT: B 650 TRP cc_start: 0.6563 (m100) cc_final: 0.5703 (m100) REVERT: B 682 ASP cc_start: 0.7583 (p0) cc_final: 0.6757 (m-30) outliers start: 26 outliers final: 19 residues processed: 118 average time/residue: 1.1233 time to fit residues: 144.0969 Evaluate side-chains 119 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 441 GLN B 54 GLN B 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.156304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133865 restraints weight = 34725.326| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.66 r_work: 0.3571 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10316 Z= 0.133 Angle : 0.505 4.804 14076 Z= 0.272 Chirality : 0.040 0.135 1648 Planarity : 0.005 0.058 1760 Dihedral : 4.982 56.384 1400 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Rotamer: Outliers : 2.52 % Allowed : 14.74 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1282 helix: 2.04 (0.18), residues: 784 sheet: -0.60 (0.66), residues: 60 loop : -1.69 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.012 0.001 TYR A 375 PHE 0.020 0.002 PHE A 183 TRP 0.008 0.001 TRP B 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00298 (10316) covalent geometry : angle 0.50531 (14076) hydrogen bonds : bond 0.04624 ( 616) hydrogen bonds : angle 4.26182 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7664 (m-40) cc_final: 0.7344 (p0) REVERT: A 183 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 184 MET cc_start: 0.8742 (mmt) cc_final: 0.8449 (mmt) REVERT: A 257 ARG cc_start: 0.6394 (mtp85) cc_final: 0.5878 (mmm-85) REVERT: A 509 ARG cc_start: 0.6573 (mmt-90) cc_final: 0.5863 (mtm180) REVERT: A 529 GLU cc_start: 0.7217 (pm20) cc_final: 0.6902 (pt0) REVERT: A 578 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6272 (ttp80) REVERT: A 629 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7526 (mptm) REVERT: A 650 TRP cc_start: 0.6607 (m100) cc_final: 0.5716 (m100) REVERT: A 682 ASP cc_start: 0.7566 (p0) cc_final: 0.6743 (m-30) REVERT: B 58 ASN cc_start: 0.7671 (m-40) cc_final: 0.7331 (p0) REVERT: B 183 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7636 (t80) REVERT: B 184 MET cc_start: 0.8761 (mmt) cc_final: 0.8466 (mmt) REVERT: B 209 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6975 (mmm160) REVERT: B 257 ARG cc_start: 0.6426 (mtp85) cc_final: 0.5906 (mmm-85) REVERT: B 509 ARG cc_start: 0.6569 (mmt-90) cc_final: 0.5857 (mtm180) REVERT: B 529 GLU cc_start: 0.7221 (pm20) cc_final: 0.6909 (pt0) REVERT: B 578 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: B 629 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7512 (mptm) REVERT: B 650 TRP cc_start: 0.6592 (m100) cc_final: 0.5695 (m100) REVERT: B 682 ASP cc_start: 0.7528 (p0) cc_final: 0.6714 (m-30) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 1.1173 time to fit residues: 142.0669 Evaluate side-chains 116 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 441 GLN B 54 GLN B 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133220 restraints weight = 34460.701| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.66 r_work: 0.3558 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10316 Z= 0.150 Angle : 0.518 4.870 14076 Z= 0.279 Chirality : 0.040 0.137 1648 Planarity : 0.006 0.060 1760 Dihedral : 5.012 57.099 1400 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 2.24 % Allowed : 15.02 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1282 helix: 1.99 (0.18), residues: 784 sheet: -0.58 (0.66), residues: 60 loop : -1.71 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.013 0.001 TYR B 95 PHE 0.020 0.002 PHE B 345 TRP 0.008 0.001 TRP B 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00345 (10316) covalent geometry : angle 0.51774 (14076) hydrogen bonds : bond 0.04815 ( 616) hydrogen bonds : angle 4.27871 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7680 (m-40) cc_final: 0.7339 (p0) REVERT: A 183 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7573 (t80) REVERT: A 184 MET cc_start: 0.8742 (mmt) cc_final: 0.8444 (mmt) REVERT: A 257 ARG cc_start: 0.6442 (mtp85) cc_final: 0.5917 (mmm-85) REVERT: A 529 GLU cc_start: 0.7234 (pm20) cc_final: 0.6930 (pt0) REVERT: A 578 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6291 (ttp80) REVERT: A 629 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7536 (mptm) REVERT: A 650 TRP cc_start: 0.6625 (m100) cc_final: 0.5736 (m100) REVERT: A 682 ASP cc_start: 0.7591 (p0) cc_final: 0.6763 (m-30) REVERT: B 58 ASN cc_start: 0.7684 (m-40) cc_final: 0.7327 (p0) REVERT: B 183 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 184 MET cc_start: 0.8759 (mmt) cc_final: 0.8459 (mmt) REVERT: B 257 ARG cc_start: 0.6450 (mtp85) cc_final: 0.5917 (mmm-85) REVERT: B 529 GLU cc_start: 0.7229 (pm20) cc_final: 0.6934 (pt0) REVERT: B 578 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6317 (ttp80) REVERT: B 629 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7518 (mptm) REVERT: B 650 TRP cc_start: 0.6598 (m100) cc_final: 0.5704 (m100) REVERT: B 682 ASP cc_start: 0.7584 (p0) cc_final: 0.6762 (m-30) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 1.1000 time to fit residues: 141.1737 Evaluate side-chains 119 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 88 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 chunk 86 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 81 GLN A 356 ASN A 441 GLN B 54 GLN B 441 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136187 restraints weight = 34902.796| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.67 r_work: 0.3584 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10316 Z= 0.106 Angle : 0.478 4.574 14076 Z= 0.255 Chirality : 0.039 0.132 1648 Planarity : 0.005 0.054 1760 Dihedral : 4.775 58.721 1400 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.93 % Rotamer: Outliers : 1.59 % Allowed : 15.67 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1282 helix: 2.27 (0.19), residues: 792 sheet: -0.62 (0.68), residues: 60 loop : -1.73 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.011 0.001 TYR A 375 PHE 0.019 0.001 PHE A 183 TRP 0.008 0.001 TRP B 55 HIS 0.004 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00231 (10316) covalent geometry : angle 0.47758 (14076) hydrogen bonds : bond 0.04076 ( 616) hydrogen bonds : angle 4.11570 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7642 (m-40) cc_final: 0.7319 (p0) REVERT: A 183 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7634 (t80) REVERT: A 184 MET cc_start: 0.8725 (mmt) cc_final: 0.8355 (mmt) REVERT: A 257 ARG cc_start: 0.6316 (mtp85) cc_final: 0.5801 (mmm-85) REVERT: A 509 ARG cc_start: 0.6561 (mmt-90) cc_final: 0.5903 (mtm180) REVERT: A 529 GLU cc_start: 0.7175 (pm20) cc_final: 0.6863 (pt0) REVERT: A 578 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6126 (ttp80) REVERT: A 629 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7465 (mptm) REVERT: A 650 TRP cc_start: 0.6593 (m100) cc_final: 0.5784 (m-10) REVERT: A 682 ASP cc_start: 0.7511 (p0) cc_final: 0.6703 (m-30) REVERT: B 58 ASN cc_start: 0.7639 (m-40) cc_final: 0.7300 (p0) REVERT: B 183 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7642 (t80) REVERT: B 184 MET cc_start: 0.8731 (mmt) cc_final: 0.8358 (mmt) REVERT: B 257 ARG cc_start: 0.6318 (mtp85) cc_final: 0.5791 (mmm-85) REVERT: B 509 ARG cc_start: 0.6564 (mmt-90) cc_final: 0.5900 (mtm180) REVERT: B 529 GLU cc_start: 0.7178 (pm20) cc_final: 0.6871 (pt0) REVERT: B 578 ARG cc_start: 0.7302 (ttp-110) cc_final: 0.6182 (ttp80) REVERT: B 629 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7465 (mptm) REVERT: B 650 TRP cc_start: 0.6574 (m100) cc_final: 0.5768 (m-10) REVERT: B 682 ASP cc_start: 0.7515 (p0) cc_final: 0.6712 (m-30) outliers start: 17 outliers final: 14 residues processed: 118 average time/residue: 1.1040 time to fit residues: 141.6938 Evaluate side-chains 116 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 750 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 441 GLN B 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133580 restraints weight = 34801.936| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.66 r_work: 0.3567 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10316 Z= 0.153 Angle : 0.512 5.093 14076 Z= 0.275 Chirality : 0.040 0.137 1648 Planarity : 0.006 0.059 1760 Dihedral : 4.918 58.411 1400 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.84 % Favored : 94.93 % Rotamer: Outliers : 1.68 % Allowed : 15.95 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1282 helix: 2.16 (0.18), residues: 782 sheet: -0.47 (0.68), residues: 60 loop : -1.65 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.013 0.001 TYR A 95 PHE 0.021 0.002 PHE B 345 TRP 0.009 0.001 TRP B 55 HIS 0.005 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00354 (10316) covalent geometry : angle 0.51157 (14076) hydrogen bonds : bond 0.04711 ( 616) hydrogen bonds : angle 4.21433 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6558.66 seconds wall clock time: 111 minutes 51.90 seconds (6711.90 seconds total)