Starting phenix.real_space_refine on Fri Jan 17 01:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmv_50571/01_2025/9fmv_50571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmv_50571/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fmv_50571/01_2025/9fmv_50571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmv_50571/01_2025/9fmv_50571.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmv_50571/01_2025/9fmv_50571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmv_50571/01_2025/9fmv_50571.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.74, per 1000 atoms: 0.75 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.02 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: 3.17 Time building geometry restraints manager: 2.88 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: 12.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.170 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- 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= 0.246 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 : 9.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.001 TRP A 633 HIS 0.009 0.001 HIS A 569 PHE 0.033 0.001 PHE A 171 TYR 0.022 0.001 TYR D 27 ARG 0.009 0.001 ARG E 66 *********************** 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 : 1.047 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: 0.2785 time to fit residues: 63.8185 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 : 1.024 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.4980 chunk 93 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.173697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147269 restraints weight = 15233.284| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.93 r_work: 0.3727 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10603 Z= 0.251 Angle : 0.577 8.818 14463 Z= 0.299 Chirality : 0.041 0.209 1608 Planarity : 0.005 0.063 1756 Dihedral : 4.665 58.817 1369 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1232 helix: 2.03 (0.17), residues: 864 sheet: -0.33 (0.57), residues: 68 loop : -0.50 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 633 HIS 0.012 0.001 HIS A 133 PHE 0.013 0.001 PHE A 369 TYR 0.026 0.001 TYR D 27 ARG 0.006 0.000 ARG D 67 *********************** 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 201 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.055 Fit side-chains REVERT: A 1 MET cc_start: 0.3922 (mmm) cc_final: 0.3699 (mmm) REVERT: A 193 MET cc_start: 0.7873 (ppp) cc_final: 0.7395 (ppp) REVERT: A 272 TRP cc_start: 0.6951 (m-10) cc_final: 0.6745 (m-10) REVERT: A 366 THR cc_start: 0.7831 (m) cc_final: 0.7529 (t) REVERT: A 565 PHE cc_start: 0.7878 (m-80) cc_final: 0.7667 (m-80) REVERT: A 570 MET cc_start: 0.7747 (mpp) cc_final: 0.7416 (mtt) REVERT: A 594 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7378 (mp0) REVERT: A 633 TRP cc_start: 0.7210 (p-90) cc_final: 0.6824 (p-90) REVERT: B 68 HIS cc_start: 0.1970 (OUTLIER) cc_final: 0.1393 (m90) REVERT: C 92 MET cc_start: 0.8119 (mtt) cc_final: 0.7897 (mtm) outliers start: 31 outliers final: 14 residues processed: 183 average time/residue: 0.2831 time to fit residues: 69.8790 Evaluate side-chains 176 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 143 LEU 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 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 104 optimal weight: 0.0980 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 0.4980 chunk 118 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 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 = 0.4174 r_free = 0.4174 target = 0.173699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147247 restraints weight = 15506.115| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.95 r_work: 0.3673 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10603 Z= 0.229 Angle : 0.557 12.870 14463 Z= 0.284 Chirality : 0.040 0.212 1608 Planarity : 0.005 0.062 1756 Dihedral : 4.644 59.204 1369 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 18.34 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1232 helix: 2.06 (0.17), residues: 865 sheet: -0.33 (0.60), residues: 68 loop : -0.64 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 58 HIS 0.009 0.001 HIS A 133 PHE 0.016 0.001 PHE A 171 TYR 0.024 0.001 TYR D 27 ARG 0.012 0.000 ARG A 463 *********************** 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 192 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.992 Fit side-chains REVERT: A 1 MET cc_start: 0.3748 (mmm) cc_final: 0.3539 (mmm) REVERT: A 155 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 193 MET cc_start: 0.7914 (ppp) cc_final: 0.7454 (ppp) REVERT: A 366 THR cc_start: 0.7905 (m) cc_final: 0.7606 (t) REVERT: A 594 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 633 TRP cc_start: 0.7153 (p-90) cc_final: 0.6873 (p-90) REVERT: A 817 LYS cc_start: 0.8065 (mttm) cc_final: 0.7764 (mtmm) REVERT: B 68 HIS cc_start: 0.1838 (OUTLIER) cc_final: 0.1288 (m90) outliers start: 29 outliers final: 16 residues processed: 173 average time/residue: 0.3008 time to fit residues: 68.7275 Evaluate side-chains 177 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 665 MET 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 75 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 28 optimal weight: 0.4980 chunk 77 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147740 restraints weight = 15257.993| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.94 r_work: 0.3681 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1409 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= 0.216 Angle : 0.546 13.105 14463 Z= 0.277 Chirality : 0.040 0.212 1608 Planarity : 0.005 0.061 1756 Dihedral : 4.379 57.628 1366 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.78 % Allowed : 18.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1232 helix: 2.11 (0.17), residues: 865 sheet: -0.30 (0.61), residues: 68 loop : -0.65 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 58 HIS 0.008 0.001 HIS A 133 PHE 0.010 0.001 PHE A 369 TYR 0.023 0.001 TYR D 27 ARG 0.007 0.000 ARG A 463 *********************** 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 209 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.041 Fit side-chains REVERT: A 1 MET cc_start: 0.3839 (mmm) cc_final: 0.3619 (mmm) REVERT: A 61 GLU cc_start: 0.7612 (mp0) cc_final: 0.7269 (mp0) REVERT: A 75 ARG cc_start: 0.7092 (tmt-80) cc_final: 0.6796 (tmt170) REVERT: A 155 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6768 (mt) REVERT: A 193 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7514 (ppp) REVERT: A 633 TRP cc_start: 0.7085 (p-90) cc_final: 0.6845 (p-90) REVERT: A 703 MET cc_start: 0.5064 (ppp) cc_final: 0.4753 (ppp) REVERT: A 817 LYS cc_start: 0.8071 (mttm) cc_final: 0.7694 (mtmm) REVERT: B 68 HIS cc_start: 0.1708 (OUTLIER) cc_final: 0.1136 (m90) REVERT: E 59 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7559 (ttt90) outliers start: 41 outliers final: 23 residues processed: 188 average time/residue: 0.2759 time to fit residues: 69.0921 Evaluate side-chains 192 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 159 SER Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 245 ILE 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 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 135 TRP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 59 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 54 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 58 optimal weight: 0.0870 chunk 100 optimal weight: 0.0670 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.1110 ------------------------------------------------------------------------------- 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 A 743 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149225 restraints weight = 15278.851| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.95 r_work: 0.3722 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10603 Z= 0.155 Angle : 0.512 12.624 14463 Z= 0.257 Chirality : 0.038 0.222 1608 Planarity : 0.004 0.059 1756 Dihedral : 4.199 56.483 1366 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.86 % Allowed : 19.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1232 helix: 2.35 (0.17), residues: 870 sheet: -0.26 (0.61), residues: 68 loop : -0.52 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 58 HIS 0.007 0.001 HIS A 117 PHE 0.012 0.001 PHE A 171 TYR 0.014 0.001 TYR C 27 ARG 0.003 0.000 ARG A 26 *********************** 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 203 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3859 (mmm) cc_final: 0.3638 (mmm) REVERT: A 61 GLU cc_start: 0.7607 (mp0) cc_final: 0.7236 (mp0) REVERT: A 75 ARG cc_start: 0.6935 (tmt-80) cc_final: 0.6705 (tmt170) REVERT: A 133 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6501 (p90) REVERT: A 193 MET cc_start: 0.7915 (ppp) cc_final: 0.7601 (ppp) REVERT: A 349 LYS cc_start: 0.8613 (mttt) cc_final: 0.8352 (mttt) REVERT: A 446 ILE cc_start: 0.8566 (pt) cc_final: 0.8359 (mt) REVERT: A 594 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 633 TRP cc_start: 0.6914 (p-90) cc_final: 0.6640 (p-90) REVERT: A 817 LYS cc_start: 0.7902 (mttm) cc_final: 0.7567 (mtmm) REVERT: B 68 HIS cc_start: 0.1752 (OUTLIER) cc_final: 0.1446 (m170) REVERT: C 61 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6814 (m-80) outliers start: 31 outliers final: 16 residues processed: 187 average time/residue: 0.2737 time to fit residues: 68.8733 Evaluate side-chains 180 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 529 PHE 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 829 PHE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain D residue 85 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN A 761 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146151 restraints weight = 15278.515| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.94 r_work: 0.3681 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10603 Z= 0.253 Angle : 0.569 14.469 14463 Z= 0.284 Chirality : 0.041 0.223 1608 Planarity : 0.005 0.058 1756 Dihedral : 4.276 54.642 1366 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.86 % Allowed : 19.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1232 helix: 2.17 (0.17), residues: 865 sheet: -0.26 (0.61), residues: 68 loop : -0.56 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 24 HIS 0.007 0.001 HIS A 133 PHE 0.015 0.001 PHE A 171 TYR 0.029 0.001 TYR D 27 ARG 0.007 0.000 ARG E 66 *********************** 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 199 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7602 (mp0) cc_final: 0.7270 (mp0) REVERT: A 75 ARG cc_start: 0.7033 (tmt-80) cc_final: 0.6476 (tmt-80) REVERT: A 133 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6473 (p90) REVERT: A 193 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: B 68 HIS cc_start: 0.1864 (OUTLIER) cc_final: 0.1629 (m170) REVERT: E 59 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7551 (ttt90) outliers start: 31 outliers final: 17 residues processed: 188 average time/residue: 0.2782 time to fit residues: 70.4017 Evaluate side-chains 184 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 254 VAL 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 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 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 135 TRP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 59 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 0.1980 chunk 119 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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 = 0.4159 r_free = 0.4159 target = 0.172529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146051 restraints weight = 15491.121| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.95 r_work: 0.3672 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10603 Z= 0.287 Angle : 0.590 15.026 14463 Z= 0.296 Chirality : 0.041 0.230 1608 Planarity : 0.005 0.058 1756 Dihedral : 4.355 52.265 1366 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.32 % Allowed : 19.82 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.24), residues: 1232 helix: 2.02 (0.17), residues: 865 sheet: -0.27 (0.61), residues: 68 loop : -0.60 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.007 0.001 HIS A 133 PHE 0.017 0.001 PHE A 171 TYR 0.029 0.001 TYR D 27 ARG 0.006 0.000 ARG E 66 *********************** 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 204 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: A 61 GLU cc_start: 0.7646 (mp0) cc_final: 0.7315 (mp0) REVERT: A 75 ARG cc_start: 0.7112 (tmt-80) cc_final: 0.6436 (tmt-80) REVERT: A 133 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6523 (p90) REVERT: A 155 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6812 (mt) REVERT: A 193 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (ppp) REVERT: A 570 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: A 594 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7244 (mp0) REVERT: A 817 LYS cc_start: 0.8158 (mttm) cc_final: 0.7920 (mtmm) REVERT: E 59 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7587 (ttt90) outliers start: 36 outliers final: 18 residues processed: 187 average time/residue: 0.2736 time to fit residues: 68.6411 Evaluate side-chains 190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 A residue 813 LEU Chi-restraints excluded: chain B residue 143 VAL 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 59 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 77 optimal weight: 0.0270 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 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 = 0.4181 r_free = 0.4181 target = 0.174490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147993 restraints weight = 15388.647| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.96 r_work: 0.3704 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10603 Z= 0.172 Angle : 0.574 15.227 14463 Z= 0.282 Chirality : 0.040 0.236 1608 Planarity : 0.005 0.061 1756 Dihedral : 4.215 50.412 1366 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.21 % Allowed : 20.92 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1232 helix: 2.24 (0.17), residues: 867 sheet: -0.21 (0.60), residues: 68 loop : -0.55 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.025 0.001 HIS A 825 PHE 0.018 0.001 PHE A 171 TYR 0.017 0.001 TYR C 27 ARG 0.007 0.000 ARG E 66 *********************** 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 189 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7625 (mp0) cc_final: 0.7275 (mp0) REVERT: A 75 ARG cc_start: 0.6996 (tmt-80) cc_final: 0.6356 (tmt-80) REVERT: A 133 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6511 (p90) REVERT: A 193 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7703 (ppp) REVERT: A 570 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7220 (mtp) REVERT: A 594 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 633 TRP cc_start: 0.6894 (p-90) cc_final: 0.6612 (p-90) REVERT: A 755 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6426 (mm-30) REVERT: A 817 LYS cc_start: 0.7976 (mttm) cc_final: 0.7653 (mtmm) outliers start: 24 outliers final: 15 residues processed: 175 average time/residue: 0.2703 time to fit residues: 64.1202 Evaluate side-chains 181 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 A residue 813 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 111 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.1878 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.174914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148561 restraints weight = 15416.682| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.94 r_work: 0.3709 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10603 Z= 0.176 Angle : 0.572 15.306 14463 Z= 0.281 Chirality : 0.039 0.231 1608 Planarity : 0.005 0.060 1756 Dihedral : 4.127 46.095 1366 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.84 % Allowed : 21.01 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1232 helix: 2.27 (0.17), residues: 870 sheet: -0.24 (0.60), residues: 68 loop : -0.50 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 633 HIS 0.015 0.001 HIS A 825 PHE 0.016 0.001 PHE A 171 TYR 0.018 0.001 TYR C 27 ARG 0.008 0.000 ARG E 66 *********************** 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 181 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7610 (mp0) cc_final: 0.7288 (mp0) REVERT: A 75 ARG cc_start: 0.6894 (tmt-80) cc_final: 0.6288 (tmt-80) REVERT: A 133 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6509 (p90) REVERT: A 181 MET cc_start: 0.7292 (tpp) cc_final: 0.6883 (tpt) REVERT: A 193 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7706 (ppp) REVERT: A 196 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6904 (mtt180) REVERT: A 349 LYS cc_start: 0.8647 (mttt) cc_final: 0.8372 (mttt) REVERT: A 570 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7230 (mtp) REVERT: A 633 TRP cc_start: 0.6877 (p-90) cc_final: 0.6552 (p-90) REVERT: A 817 LYS cc_start: 0.7901 (mttm) cc_final: 0.7583 (mtmm) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.3159 time to fit residues: 73.3373 Evaluate side-chains 180 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.0870 chunk 58 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 0.0020 chunk 103 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.2566 ------------------------------------------------------------------------------- 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 459 HIS ** 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 = 0.4182 r_free = 0.4182 target = 0.174402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147939 restraints weight = 15388.321| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.95 r_work: 0.3702 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1959 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= 0.197 Angle : 0.592 16.124 14463 Z= 0.291 Chirality : 0.040 0.229 1608 Planarity : 0.005 0.060 1756 Dihedral : 4.107 42.129 1366 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.24), residues: 1232 helix: 2.24 (0.17), residues: 869 sheet: -0.17 (0.61), residues: 68 loop : -0.48 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.014 0.001 HIS A 825 PHE 0.010 0.001 PHE A 369 TYR 0.021 0.001 TYR C 27 ARG 0.009 0.000 ARG E 66 ********************** 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 184 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7620 (mp0) cc_final: 0.7298 (mp0) REVERT: A 75 ARG cc_start: 0.6939 (tmt-80) cc_final: 0.6356 (tmt-80) REVERT: A 133 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6494 (p90) REVERT: A 181 MET cc_start: 0.7350 (tpp) cc_final: 0.6916 (tpt) REVERT: A 193 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7700 (ppp) REVERT: A 196 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6971 (mtt180) REVERT: A 570 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: A 633 TRP cc_start: 0.6894 (p-90) cc_final: 0.6539 (p-90) REVERT: A 817 LYS cc_start: 0.7957 (mttm) cc_final: 0.7635 (mtmm) outliers start: 19 outliers final: 15 residues processed: 175 average time/residue: 0.2752 time to fit residues: 64.8961 Evaluate side-chains 181 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.2980 chunk 31 optimal weight: 0.2980 chunk 117 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 459 HIS A 490 HIS ** A 678 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.172944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146562 restraints weight = 15128.034| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.92 r_work: 0.3672 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10603 Z= 0.264 Angle : 0.621 16.736 14463 Z= 0.309 Chirality : 0.042 0.234 1608 Planarity : 0.005 0.059 1756 Dihedral : 4.198 38.359 1366 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.21 % Allowed : 21.11 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.24), residues: 1232 helix: 2.05 (0.17), residues: 865 sheet: -0.29 (0.61), residues: 68 loop : -0.56 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.013 0.001 HIS A 825 PHE 0.028 0.001 PHE A 171 TYR 0.028 0.001 TYR D 27 ARG 0.008 0.001 ARG E 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.50 seconds wall clock time: 111 minutes 36.42 seconds (6696.42 seconds total)