Starting phenix.real_space_refine on Wed Sep 17 17:56:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmv_50571/09_2025/9fmv_50571.map" } resolution = 3.43 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6848 2.51 5 N 1740 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10272 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 6272 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 39, 'TRANS': 737} Chain breaks: 6 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1205 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1205 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "D" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1205 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "E" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 385 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Time building chain proxies: 2.56, per 1000 atoms: 0.25 Number of scatterers: 10272 At special positions: 0 Unit cell: (107.392, 119.138, 153.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1641 8.00 N 1740 7.00 C 6848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 379.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 73.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.650A pdb=" N THR A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.803A pdb=" N HIS A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 48 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.889A pdb=" N GLU A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 77 through 92 Processing helix chain 'A' and resid 106 through 134 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 144 through 168 Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.555A pdb=" N ARG A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.534A pdb=" N THR A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 254 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 285 through 298 removed outlier: 3.901A pdb=" N ASN A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.663A pdb=" N LYS A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.532A pdb=" N MET A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.577A pdb=" N MET A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 517 through 531 Processing helix chain 'A' and resid 534 through 549 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 558 through 582 Proline residue: A 568 - end of helix Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.622A pdb=" N TYR A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 removed outlier: 3.578A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 removed outlier: 3.520A pdb=" N ILE A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 650 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 664 through 692 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 810 through 830 Processing helix chain 'A' and resid 831 through 850 removed outlier: 4.626A pdb=" N ILE A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 22 through 37 removed outlier: 4.063A pdb=" N PHE B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 60 through 83 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 87 through 101 removed outlier: 5.047A pdb=" N SER B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 115 through 133 Processing helix chain 'B' and resid 137 through 155 removed outlier: 4.113A pdb=" N PHE B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 23 through 37 removed outlier: 3.702A pdb=" N TYR C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 60 through 83 Proline residue: C 73 - end of helix Processing helix chain 'C' and resid 87 through 101 removed outlier: 5.280A pdb=" N SER C 96 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 101 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 115 through 133 Processing helix chain 'C' and resid 137 through 155 Processing helix chain 'D' and resid 22 through 38 removed outlier: 4.216A pdb=" N PHE D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 27 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 55 Processing helix chain 'D' and resid 60 through 83 Proline residue: D 73 - end of helix Processing helix chain 'D' and resid 87 through 101 removed outlier: 4.354A pdb=" N SER D 96 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 115 through 136 Processing helix chain 'D' and resid 138 through 155 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.946A pdb=" N LEU E 31 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331 removed outlier: 8.798A pdb=" N LYS A 329 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 308 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE A 331 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE A 310 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 275 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TRP A 309 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 277 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 311 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 279 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP A 276 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 436 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 384 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA A 472 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N MET A 386 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 706 through 710 removed outlier: 6.791A pdb=" N GLY A 730 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE A 724 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS A 773 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 762 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS A 750 " --> pdb=" O PRO A 706 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 2022 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: 1.70 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3112 1.34 - 1.46: 2867 1.46 - 1.58: 4549 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 10603 Sorted by residual: bond pdb=" CB PRO A 604 " pdb=" CG PRO A 604 " ideal model delta sigma weight residual 1.492 1.401 0.091 5.00e-02 4.00e+02 3.34e+00 bond pdb=" CG1 ILE A 815 " pdb=" CD1 ILE A 815 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.20e+00 bond pdb=" CA PRO A 603 " pdb=" C PRO A 603 " ideal model delta sigma weight residual 1.517 1.530 -0.013 9.30e-03 1.16e+04 1.98e+00 bond pdb=" CG LEU E 52 " pdb=" CD2 LEU E 52 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" C PRO A 603 " pdb=" N PRO A 604 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.51e+00 ... (remaining 10598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 14261 2.31 - 4.62: 162 4.62 - 6.93: 28 6.93 - 9.24: 9 9.24 - 11.55: 3 Bond angle restraints: 14463 Sorted by residual: angle pdb=" N PRO A 603 " pdb=" CA PRO A 603 " pdb=" C PRO A 603 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" CA PRO A 603 " pdb=" C PRO A 603 " pdb=" N PRO A 604 " ideal model delta sigma weight residual 117.93 124.45 -6.52 1.20e+00 6.94e-01 2.95e+01 angle pdb=" C SER D 22 " pdb=" CA SER D 22 " pdb=" CB SER D 22 " ideal model delta sigma weight residual 117.23 110.25 6.98 1.36e+00 5.41e-01 2.64e+01 angle pdb=" C SER B 22 " pdb=" CA SER B 22 " pdb=" CB SER B 22 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 110.62 106.44 4.18 1.02e+00 9.61e-01 1.68e+01 ... (remaining 14458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5317 17.88 - 35.76: 582 35.76 - 53.65: 117 53.65 - 71.53: 17 71.53 - 89.41: 7 Dihedral angle restraints: 6040 sinusoidal: 2398 harmonic: 3642 Sorted by residual: dihedral pdb=" CA THR A 373 " pdb=" C THR A 373 " pdb=" N MET A 374 " pdb=" CA MET A 374 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ARG A 711 " pdb=" C ARG A 711 " pdb=" N GLU A 712 " pdb=" CA GLU A 712 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO A 603 " pdb=" C PRO A 603 " pdb=" N PRO A 604 " pdb=" CA PRO A 604 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1448 0.067 - 0.134: 148 0.134 - 0.201: 9 0.201 - 0.268: 1 0.268 - 0.335: 2 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CG LEU D 147 " pdb=" CB LEU D 147 " pdb=" CD1 LEU D 147 " pdb=" CD2 LEU D 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA PRO A 603 " pdb=" N PRO A 603 " pdb=" C PRO A 603 " pdb=" CB PRO A 603 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 155 " pdb=" CA ILE A 155 " pdb=" CG1 ILE A 155 " pdb=" CG2 ILE A 155 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1605 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 567 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 568 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 263 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 264 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 172 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 173 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.036 5.00e-02 4.00e+02 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1001 2.74 - 3.28: 10328 3.28 - 3.82: 17501 3.82 - 4.36: 18879 4.36 - 4.90: 32868 Nonbonded interactions: 80577 Sorted by model distance: nonbonded pdb=" O MET D 56 " pdb=" NH1 ARG D 67 " model vdw 2.203 3.120 nonbonded pdb=" O LEU A 348 " pdb=" NH2 ARG A 440 " model vdw 2.209 3.120 nonbonded pdb=" O LEU A 143 " pdb=" NH1 ARG A 148 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR C 27 " pdb=" O GLY C 75 " model vdw 2.264 3.040 nonbonded pdb=" NH2 ARG A 54 " pdb=" OE1 GLN D 16 " model vdw 2.267 3.120 ... (remaining 80572 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: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 9.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10603 Z= 0.159 Angle : 0.645 11.549 14463 Z= 0.345 Chirality : 0.043 0.335 1608 Planarity : 0.006 0.087 1756 Dihedral : 15.229 89.412 3684 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.55 % Allowed : 18.99 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1232 helix: 1.77 (0.17), residues: 853 sheet: -0.11 (0.59), residues: 67 loop : -0.59 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 66 TYR 0.022 0.001 TYR D 27 PHE 0.033 0.001 PHE A 171 TRP 0.034 0.001 TRP A 633 HIS 0.009 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00364 (10603) covalent geometry : angle 0.64521 (14463) hydrogen bonds : bond 0.14814 ( 683) hydrogen bonds : angle 5.77401 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.369 Fit side-chains REVERT: A 374 MET cc_start: 0.8637 (mmm) cc_final: 0.7876 (mmm) REVERT: A 594 GLU cc_start: 0.7087 (mp0) cc_final: 0.6751 (mp0) REVERT: A 603 PRO cc_start: 0.8835 (Cg_endo) cc_final: 0.8577 (Cg_exo) outliers start: 6 outliers final: 2 residues processed: 171 average time/residue: 0.1349 time to fit residues: 30.7687 Evaluate side-chains 166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 336 HIS A 371 GLN A 569 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 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 = 0.4176 r_free = 0.4176 target = 0.173782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147241 restraints weight = 15361.606| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.94 r_work: 0.3722 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10603 Z= 0.165 Angle : 0.578 9.034 14463 Z= 0.300 Chirality : 0.041 0.212 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.664 59.138 1369 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.58 % Allowed : 17.42 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.24), residues: 1232 helix: 2.02 (0.17), residues: 865 sheet: -0.33 (0.57), residues: 68 loop : -0.51 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 67 TYR 0.026 0.001 TYR D 27 PHE 0.013 0.001 PHE A 369 TRP 0.017 0.001 TRP A 633 HIS 0.012 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00378 (10603) covalent geometry : angle 0.57776 (14463) hydrogen bonds : bond 0.04741 ( 683) hydrogen bonds : angle 4.32606 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.399 Fit side-chains REVERT: A 1 MET cc_start: 0.3920 (mmm) cc_final: 0.3700 (mmm) REVERT: A 193 MET cc_start: 0.7869 (ppp) cc_final: 0.7387 (ppp) REVERT: A 272 TRP cc_start: 0.6953 (m-10) cc_final: 0.6725 (m-10) REVERT: A 366 THR cc_start: 0.7828 (m) cc_final: 0.7523 (t) REVERT: A 594 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7361 (mp0) REVERT: A 817 LYS cc_start: 0.8100 (mttt) cc_final: 0.7812 (mtmm) REVERT: B 68 HIS cc_start: 0.1985 (OUTLIER) cc_final: 0.1415 (m90) REVERT: C 92 MET cc_start: 0.8121 (mtt) cc_final: 0.7907 (mtm) outliers start: 28 outliers final: 12 residues processed: 182 average time/residue: 0.1294 time to fit residues: 31.6019 Evaluate side-chains 175 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 0.0670 chunk 114 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 223 ASN A 371 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147229 restraints weight = 15446.608| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.95 r_work: 0.3676 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10603 Z= 0.147 Angle : 0.551 11.828 14463 Z= 0.281 Chirality : 0.040 0.215 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.627 59.352 1369 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.86 % Allowed : 17.88 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.24), residues: 1232 helix: 2.07 (0.17), residues: 865 sheet: -0.36 (0.60), residues: 68 loop : -0.64 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.023 0.001 TYR D 27 PHE 0.015 0.001 PHE A 171 TRP 0.013 0.001 TRP E 58 HIS 0.009 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00340 (10603) covalent geometry : angle 0.55128 (14463) hydrogen bonds : bond 0.04345 ( 683) hydrogen bonds : angle 4.13810 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.375 Fit side-chains REVERT: A 1 MET cc_start: 0.3752 (mmm) cc_final: 0.3541 (mmm) REVERT: A 155 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 193 MET cc_start: 0.7934 (ppp) cc_final: 0.7471 (ppp) REVERT: A 366 THR cc_start: 0.7900 (m) cc_final: 0.7593 (t) REVERT: A 594 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 633 TRP cc_start: 0.7145 (p-90) cc_final: 0.6798 (p-90) REVERT: B 68 HIS cc_start: 0.1838 (OUTLIER) cc_final: 0.1285 (m90) outliers start: 31 outliers final: 17 residues processed: 177 average time/residue: 0.1357 time to fit residues: 31.8944 Evaluate side-chains 181 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 56 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 371 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN A 825 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.174417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147724 restraints weight = 15503.080| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.97 r_work: 0.3681 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10603 Z= 0.131 Angle : 0.535 12.318 14463 Z= 0.272 Chirality : 0.040 0.211 1608 Planarity : 0.005 0.060 1756 Dihedral : 4.354 57.787 1366 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 18.43 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.24), residues: 1232 helix: 2.13 (0.17), residues: 866 sheet: -0.28 (0.61), residues: 68 loop : -0.65 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 73 TYR 0.021 0.001 TYR C 27 PHE 0.010 0.001 PHE A 369 TRP 0.012 0.001 TRP E 58 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00301 (10603) covalent geometry : angle 0.53461 (14463) hydrogen bonds : bond 0.04057 ( 683) hydrogen bonds : angle 4.00316 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.413 Fit side-chains REVERT: A 1 MET cc_start: 0.3894 (mmm) cc_final: 0.3665 (mmm) REVERT: A 61 GLU cc_start: 0.7600 (mp0) cc_final: 0.7260 (mp0) REVERT: A 75 ARG cc_start: 0.7091 (tmt-80) cc_final: 0.6855 (tmt170) REVERT: A 155 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6744 (mt) REVERT: A 193 MET cc_start: 0.7935 (ppp) cc_final: 0.7533 (ppp) REVERT: A 594 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 633 TRP cc_start: 0.7096 (p-90) cc_final: 0.6858 (p-90) REVERT: A 703 MET cc_start: 0.5104 (ppp) cc_final: 0.4799 (ppp) REVERT: A 817 LYS cc_start: 0.8032 (mttm) cc_final: 0.7750 (mtmm) REVERT: B 68 HIS cc_start: 0.1718 (OUTLIER) cc_final: 0.1153 (m90) outliers start: 37 outliers final: 20 residues processed: 188 average time/residue: 0.1244 time to fit residues: 31.0118 Evaluate side-chains 187 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145490 restraints weight = 15362.398| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.95 r_work: 0.3652 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10603 Z= 0.200 Angle : 0.592 15.420 14463 Z= 0.301 Chirality : 0.042 0.223 1608 Planarity : 0.005 0.061 1756 Dihedral : 4.486 56.107 1366 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.96 % Allowed : 18.34 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.24), residues: 1232 helix: 1.93 (0.17), residues: 865 sheet: -0.22 (0.62), residues: 67 loop : -0.65 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 66 TYR 0.032 0.001 TYR D 27 PHE 0.017 0.002 PHE A 171 TRP 0.016 0.001 TRP D 24 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00470 (10603) covalent geometry : angle 0.59185 (14463) hydrogen bonds : bond 0.04614 ( 683) hydrogen bonds : angle 4.14954 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.389 Fit side-chains REVERT: A 1 MET cc_start: 0.3900 (mmm) cc_final: 0.3680 (mmm) REVERT: A 61 GLU cc_start: 0.7647 (mp0) cc_final: 0.7301 (mp0) REVERT: A 75 ARG cc_start: 0.7174 (tmt-80) cc_final: 0.6357 (tmt-80) REVERT: A 133 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6515 (p90) REVERT: A 155 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6877 (mt) REVERT: A 193 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7605 (ppp) REVERT: A 594 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 817 LYS cc_start: 0.8222 (mttm) cc_final: 0.7909 (mtmm) REVERT: A 821 ARG cc_start: 0.7101 (ptm-80) cc_final: 0.6742 (ttt-90) REVERT: B 68 HIS cc_start: 0.1836 (OUTLIER) cc_final: 0.1566 (m170) REVERT: C 92 MET cc_start: 0.8319 (mtm) cc_final: 0.8102 (mtm) outliers start: 43 outliers final: 21 residues processed: 195 average time/residue: 0.1342 time to fit residues: 34.9103 Evaluate side-chains 195 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 0.4980 chunk 56 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 223 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.173410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146914 restraints weight = 15524.506| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.96 r_work: 0.3671 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10603 Z= 0.140 Angle : 0.558 13.435 14463 Z= 0.281 Chirality : 0.040 0.236 1608 Planarity : 0.005 0.059 1756 Dihedral : 4.398 55.358 1366 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.13 % Allowed : 19.63 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.24), residues: 1232 helix: 2.08 (0.17), residues: 865 sheet: -0.27 (0.63), residues: 68 loop : -0.64 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.021 0.001 TYR D 27 PHE 0.014 0.001 PHE A 171 TRP 0.015 0.001 TRP A 633 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00328 (10603) covalent geometry : angle 0.55802 (14463) hydrogen bonds : bond 0.04150 ( 683) hydrogen bonds : angle 4.03303 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.389 Fit side-chains REVERT: A 1 MET cc_start: 0.3896 (mmm) cc_final: 0.3683 (mmm) REVERT: A 51 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6437 (pm20) REVERT: A 61 GLU cc_start: 0.7630 (mp0) cc_final: 0.7274 (mp0) REVERT: A 75 ARG cc_start: 0.7109 (tmt-80) cc_final: 0.6497 (tmt170) REVERT: A 133 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6499 (p90) REVERT: A 155 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 193 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7631 (ppp) REVERT: A 570 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7208 (mtp) REVERT: A 594 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 817 LYS cc_start: 0.8113 (mttm) cc_final: 0.7734 (mtmm) REVERT: B 68 HIS cc_start: 0.1871 (OUTLIER) cc_final: 0.1656 (m170) outliers start: 34 outliers final: 18 residues processed: 187 average time/residue: 0.1321 time to fit residues: 32.9018 Evaluate side-chains 194 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.3980 chunk 120 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 223 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145763 restraints weight = 15281.395| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.93 r_work: 0.3669 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10603 Z= 0.189 Angle : 0.611 15.660 14463 Z= 0.304 Chirality : 0.042 0.241 1608 Planarity : 0.005 0.059 1756 Dihedral : 4.454 53.410 1366 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.69 % Allowed : 19.08 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.24), residues: 1232 helix: 1.93 (0.17), residues: 865 sheet: -0.22 (0.62), residues: 67 loop : -0.63 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 66 TYR 0.028 0.001 TYR D 27 PHE 0.015 0.001 PHE A 171 TRP 0.021 0.001 TRP A 633 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00447 (10603) covalent geometry : angle 0.61077 (14463) hydrogen bonds : bond 0.04475 ( 683) hydrogen bonds : angle 4.13653 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3909 (mmm) cc_final: 0.3700 (mmm) REVERT: A 51 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: A 61 GLU cc_start: 0.7638 (mp0) cc_final: 0.7313 (mp0) REVERT: A 75 ARG cc_start: 0.7203 (tmt-80) cc_final: 0.6534 (tmt170) REVERT: A 133 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6525 (p90) REVERT: A 155 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 193 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7625 (ppp) REVERT: A 570 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7255 (mtp) REVERT: A 594 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 817 LYS cc_start: 0.8207 (mttm) cc_final: 0.7929 (mtmm) outliers start: 40 outliers final: 26 residues processed: 195 average time/residue: 0.1286 time to fit residues: 33.5553 Evaluate side-chains 202 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 76 optimal weight: 0.2980 chunk 94 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 47 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 223 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.173359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146992 restraints weight = 15314.870| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.93 r_work: 0.3686 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10603 Z= 0.143 Angle : 0.586 14.938 14463 Z= 0.291 Chirality : 0.040 0.241 1608 Planarity : 0.005 0.059 1756 Dihedral : 4.367 51.818 1366 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 19.17 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.24), residues: 1232 helix: 2.04 (0.17), residues: 865 sheet: -0.32 (0.61), residues: 68 loop : -0.64 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 463 TYR 0.020 0.001 TYR D 27 PHE 0.017 0.001 PHE A 171 TRP 0.024 0.001 TRP A 633 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00333 (10603) covalent geometry : angle 0.58597 (14463) hydrogen bonds : bond 0.04147 ( 683) hydrogen bonds : angle 4.04497 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: A 61 GLU cc_start: 0.7642 (mp0) cc_final: 0.7298 (mp0) REVERT: A 75 ARG cc_start: 0.7194 (tmt-80) cc_final: 0.6529 (tmt170) REVERT: A 133 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6482 (p90) REVERT: A 155 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6843 (mt) REVERT: A 193 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7618 (ppp) REVERT: A 570 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7192 (mtp) REVERT: A 594 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 817 LYS cc_start: 0.8109 (mttm) cc_final: 0.7863 (mtmm) outliers start: 37 outliers final: 25 residues processed: 187 average time/residue: 0.1275 time to fit residues: 32.1084 Evaluate side-chains 195 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 78 optimal weight: 0.0870 chunk 105 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 69 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 overall best weight: 0.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 223 ASN A 646 ASN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149582 restraints weight = 15285.497| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.93 r_work: 0.3721 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10603 Z= 0.109 Angle : 0.560 14.161 14463 Z= 0.277 Chirality : 0.039 0.233 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.181 47.712 1366 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 20.09 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.24), residues: 1232 helix: 2.28 (0.17), residues: 869 sheet: -0.15 (0.60), residues: 68 loop : -0.58 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 463 TYR 0.012 0.001 TYR C 27 PHE 0.016 0.001 PHE A 171 TRP 0.035 0.001 TRP A 633 HIS 0.006 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00240 (10603) covalent geometry : angle 0.55980 (14463) hydrogen bonds : bond 0.03605 ( 683) hydrogen bonds : angle 3.86988 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7595 (mp0) cc_final: 0.7235 (mp0) REVERT: A 75 ARG cc_start: 0.7048 (tmt-80) cc_final: 0.6473 (tmt170) REVERT: A 133 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6468 (p90) REVERT: A 193 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7700 (ppp) REVERT: A 205 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 349 LYS cc_start: 0.8637 (mttt) cc_final: 0.8394 (mttt) REVERT: A 594 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 633 TRP cc_start: 0.6817 (p-90) cc_final: 0.6109 (p-90) REVERT: A 817 LYS cc_start: 0.7916 (mttm) cc_final: 0.7594 (mtmm) REVERT: A 824 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7280 (mtp180) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 0.1274 time to fit residues: 31.6963 Evaluate side-chains 183 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 99 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145814 restraints weight = 15254.369| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.93 r_work: 0.3663 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10603 Z= 0.208 Angle : 0.644 16.569 14463 Z= 0.320 Chirality : 0.043 0.236 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.357 44.521 1366 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.12 % Allowed : 20.28 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.24), residues: 1232 helix: 1.90 (0.17), residues: 865 sheet: -0.21 (0.61), residues: 67 loop : -0.67 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 66 TYR 0.031 0.001 TYR D 27 PHE 0.014 0.002 PHE C 42 TRP 0.026 0.001 TRP A 633 HIS 0.028 0.002 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00494 (10603) covalent geometry : angle 0.64379 (14463) hydrogen bonds : bond 0.04535 ( 683) hydrogen bonds : angle 4.15700 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.398 Fit side-chains REVERT: A 61 GLU cc_start: 0.7623 (mp0) cc_final: 0.7282 (mp0) REVERT: A 75 ARG cc_start: 0.7090 (tmt-80) cc_final: 0.6412 (tmt-80) REVERT: A 133 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6504 (p90) REVERT: A 155 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6816 (mt) REVERT: A 193 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: A 570 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: A 594 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 817 LYS cc_start: 0.8155 (mttm) cc_final: 0.7896 (mtmm) REVERT: C 150 ASN cc_start: 0.8273 (m-40) cc_final: 0.8055 (m-40) outliers start: 23 outliers final: 15 residues processed: 183 average time/residue: 0.1315 time to fit residues: 32.1505 Evaluate side-chains 189 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 118 optimal weight: 0.0980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 291 ASN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147768 restraints weight = 15380.829| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.94 r_work: 0.3698 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10603 Z= 0.128 Angle : 0.586 15.569 14463 Z= 0.292 Chirality : 0.040 0.241 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.244 40.829 1366 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.75 % Allowed : 21.29 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.24), residues: 1232 helix: 2.04 (0.17), residues: 865 sheet: -0.28 (0.61), residues: 68 loop : -0.62 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 66 TYR 0.017 0.001 TYR C 27 PHE 0.029 0.001 PHE A 171 TRP 0.025 0.001 TRP A 633 HIS 0.018 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00294 (10603) covalent geometry : angle 0.58603 (14463) hydrogen bonds : bond 0.03989 ( 683) hydrogen bonds : angle 4.02503 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.31 seconds wall clock time: 58 minutes 56.57 seconds (3536.57 seconds total)