Starting phenix.real_space_refine on Thu Sep 26 12:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/09_2024/7n6r_24209.cif" } resolution = 3.93 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= 0.005 sd= 1.015 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 100 5.16 5 C 8656 2.51 5 N 2004 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "B" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "C" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "D" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.46, per 1000 atoms: 0.67 Number of scatterers: 12708 At special positions: 0 Unit cell: (112.455, 184.093, 74.97, 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 100 16.00 O 1948 8.00 N 2004 7.00 C 8656 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: 3.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.647A pdb=" N ARG A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 162 through 189 Proline residue: A 172 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.805A pdb=" N ALA A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 226 through 255 removed outlier: 4.340A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.587A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.597A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.631A pdb=" N PHE A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.745A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.890A pdb=" N ARG A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.468A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.634A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.837A pdb=" N PHE A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 499 removed outlier: 4.171A pdb=" N MET A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 117 through 144 removed outlier: 3.638A pdb=" N ARG B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 162 through 189 Proline residue: B 172 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.821A pdb=" N ALA B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 225 through 255 removed outlier: 4.039A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.591A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 293 through 318 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.583A pdb=" N PHE B 323 " --> pdb=" O CYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.727A pdb=" N LEU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.893A pdb=" N ARG B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 4.456A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.581A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 462 removed outlier: 3.814A pdb=" N PHE B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 499 removed outlier: 4.176A pdb=" N MET B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 143 removed outlier: 3.652A pdb=" N ARG C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 162 through 189 Proline residue: C 172 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.803A pdb=" N ALA C 205 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 226 through 255 removed outlier: 4.319A pdb=" N LEU C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Proline residue: C 252 - end of helix removed outlier: 3.587A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.604A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 318 Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.632A pdb=" N PHE C 323 " --> pdb=" O CYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.751A pdb=" N LEU C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 360 Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 406 through 415 removed outlier: 3.904A pdb=" N ARG C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 423 removed outlier: 4.469A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.627A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 462 removed outlier: 3.834A pdb=" N PHE C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 499 removed outlier: 4.170A pdb=" N MET C 477 " --> pdb=" O TRP C 473 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 117 through 144 removed outlier: 3.637A pdb=" N ARG D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 162 through 189 Proline residue: D 172 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.824A pdb=" N ALA D 205 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 225 through 255 removed outlier: 4.040A pdb=" N LEU D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Proline residue: D 252 - end of helix removed outlier: 3.591A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 293 through 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.583A pdb=" N PHE D 323 " --> pdb=" O CYS D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.729A pdb=" N LEU D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.895A pdb=" N ARG D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 removed outlier: 4.455A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.579A pdb=" N HIS D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 462 removed outlier: 3.814A pdb=" N PHE D 462 " --> pdb=" O GLY D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 499 removed outlier: 4.175A pdb=" N MET D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 497 " --> pdb=" O CYS D 493 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2340 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: 3.48 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1976 1.33 - 1.45: 3818 1.45 - 1.57: 7154 1.57 - 1.69: 16 1.69 - 1.82: 156 Bond restraints: 13120 Sorted by residual: bond pdb=" C19 ROV D 601 " pdb=" C20 ROV D 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C19 ROV A 601 " pdb=" C20 ROV A 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C19 ROV B 601 " pdb=" C20 ROV B 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C19 ROV C 601 " pdb=" C20 ROV C 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C18 ROV C 601 " pdb=" C22 ROV C 601 " ideal model delta sigma weight residual 1.538 1.374 0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11279 1.54 - 3.08: 4970 3.08 - 4.62: 1367 4.62 - 6.16: 225 6.16 - 7.70: 23 Bond angle restraints: 17864 Sorted by residual: angle pdb=" C GLY D 457 " pdb=" N GLY D 458 " pdb=" CA GLY D 458 " ideal model delta sigma weight residual 120.03 125.62 -5.59 1.12e+00 7.97e-01 2.49e+01 angle pdb=" C GLY B 457 " pdb=" N GLY B 458 " pdb=" CA GLY B 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY A 457 " pdb=" N GLY A 458 " pdb=" CA GLY A 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY C 457 " pdb=" N GLY C 458 " pdb=" CA GLY C 458 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.46e+01 angle pdb=" C LEU A 199 " pdb=" N GLY A 200 " pdb=" CA GLY A 200 " ideal model delta sigma weight residual 120.03 125.12 -5.09 1.12e+00 7.97e-01 2.07e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6961 17.71 - 35.41: 693 35.41 - 53.12: 170 53.12 - 70.83: 34 70.83 - 88.53: 18 Dihedral angle restraints: 7876 sinusoidal: 3468 harmonic: 4408 Sorted by residual: dihedral pdb=" CA VAL D 117 " pdb=" C VAL D 117 " pdb=" N GLN D 118 " pdb=" CA GLN D 118 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA VAL C 117 " pdb=" C VAL C 117 " pdb=" N GLN C 118 " pdb=" CA GLN C 118 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1009 0.058 - 0.116: 715 0.116 - 0.173: 233 0.173 - 0.231: 15 0.231 - 0.289: 12 Chirality restraints: 1984 Sorted by residual: chirality pdb=" C13 CLR A 603 " pdb=" C12 CLR A 603 " pdb=" C14 CLR A 603 " pdb=" C17 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C13 CLR D 602 " pdb=" C12 CLR D 602 " pdb=" C14 CLR D 602 " pdb=" C17 CLR D 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C13 CLR B 603 " pdb=" C12 CLR B 603 " pdb=" C14 CLR B 603 " pdb=" C17 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1981 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 490 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C SER A 490 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 490 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 490 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C SER C 490 " 0.035 2.00e-02 2.50e+03 pdb=" O SER C 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 491 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 490 " -0.009 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C SER B 490 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 491 " -0.012 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1339 2.79 - 3.32: 13402 3.32 - 3.85: 19526 3.85 - 4.37: 24118 4.37 - 4.90: 40058 Nonbonded interactions: 98443 Sorted by model distance: nonbonded pdb=" O ILE C 281 " pdb=" OH TYR C 286 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A 281 " pdb=" OH TYR A 286 " model vdw 2.264 3.040 nonbonded pdb=" O ILE D 281 " pdb=" OH TYR D 286 " model vdw 2.282 3.040 nonbonded pdb=" O ILE B 281 " pdb=" OH TYR B 286 " model vdw 2.283 3.040 nonbonded pdb=" NE2 GLN D 236 " pdb=" OH TYR D 436 " model vdw 2.395 3.120 ... (remaining 98438 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 'A' selection = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.800 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.015 0.167 13120 Z= 0.986 Angle : 1.794 7.702 17864 Z= 1.333 Chirality : 0.078 0.289 1984 Planarity : 0.004 0.020 2108 Dihedral : 15.717 88.533 5028 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.14 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 8.20 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.93 (0.18), residues: 1460 helix: -2.25 (0.13), residues: 1044 sheet: None (None), residues: 0 loop : -3.07 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 401 HIS 0.008 0.002 HIS C 119 PHE 0.028 0.003 PHE C 444 TYR 0.020 0.003 TYR A 271 ARG 0.003 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 393 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8215 (mt0) cc_final: 0.7946 (mp10) REVERT: A 122 THR cc_start: 0.8837 (m) cc_final: 0.8574 (m) REVERT: A 135 ILE cc_start: 0.7723 (tt) cc_final: 0.7488 (tt) REVERT: A 284 GLU cc_start: 0.8457 (pp20) cc_final: 0.7832 (pt0) REVERT: A 374 ASP cc_start: 0.7715 (t0) cc_final: 0.7342 (t0) REVERT: A 442 LEU cc_start: 0.8203 (mt) cc_final: 0.7987 (mt) REVERT: A 444 PHE cc_start: 0.6957 (m-80) cc_final: 0.6523 (m-80) REVERT: A 480 MET cc_start: 0.7851 (mmt) cc_final: 0.7094 (tmm) REVERT: B 169 THR cc_start: 0.8313 (t) cc_final: 0.8077 (p) REVERT: B 170 TRP cc_start: 0.8127 (t60) cc_final: 0.7351 (t60) REVERT: B 247 LEU cc_start: 0.9193 (mm) cc_final: 0.8805 (tt) REVERT: B 274 PHE cc_start: 0.8400 (t80) cc_final: 0.8134 (t80) REVERT: B 350 MET cc_start: 0.7928 (mmm) cc_final: 0.6976 (tmm) REVERT: B 360 HIS cc_start: 0.8052 (t70) cc_final: 0.7311 (t70) REVERT: B 380 ASP cc_start: 0.7305 (p0) cc_final: 0.6611 (p0) REVERT: B 381 TRP cc_start: 0.9071 (p-90) cc_final: 0.8842 (p-90) REVERT: B 393 THR cc_start: 0.8673 (p) cc_final: 0.7810 (t) REVERT: B 419 ARG cc_start: 0.5983 (ptt-90) cc_final: 0.4807 (ptm160) REVERT: B 423 MET cc_start: 0.8165 (ttp) cc_final: 0.7944 (tpp) REVERT: B 435 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: B 473 TRP cc_start: 0.7827 (t-100) cc_final: 0.6694 (m-90) REVERT: C 115 MET cc_start: 0.8317 (tpt) cc_final: 0.8111 (tpt) REVERT: C 374 ASP cc_start: 0.7769 (t0) cc_final: 0.7198 (t0) REVERT: C 444 PHE cc_start: 0.7026 (m-80) cc_final: 0.6510 (m-80) REVERT: D 102 LYS cc_start: 0.7984 (tttm) cc_final: 0.7476 (tppt) REVERT: D 170 TRP cc_start: 0.8076 (t60) cc_final: 0.7051 (t60) REVERT: D 247 LEU cc_start: 0.9139 (mm) cc_final: 0.8730 (tt) REVERT: D 266 PRO cc_start: 0.7397 (Cg_endo) cc_final: 0.6564 (Cg_exo) REVERT: D 379 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7043 (mtp85) REVERT: D 380 ASP cc_start: 0.6825 (p0) cc_final: 0.6510 (p0) REVERT: D 391 TYR cc_start: 0.7876 (m-80) cc_final: 0.7487 (t80) REVERT: D 393 THR cc_start: 0.8475 (p) cc_final: 0.7616 (t) REVERT: D 428 LEU cc_start: 0.8825 (tp) cc_final: 0.8594 (pp) REVERT: D 435 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: D 473 TRP cc_start: 0.7937 (t-100) cc_final: 0.6625 (m-90) REVERT: D 476 LEU cc_start: 0.8259 (tt) cc_final: 0.7426 (mm) outliers start: 16 outliers final: 3 residues processed: 401 average time/residue: 0.2420 time to fit residues: 137.6653 Evaluate side-chains 273 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 435 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 236 GLN B 207 HIS B 217 HIS B 236 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 207 HIS C 236 GLN D 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13120 Z= 0.218 Angle : 0.722 10.081 17864 Z= 0.345 Chirality : 0.041 0.142 1984 Planarity : 0.005 0.039 2108 Dihedral : 9.326 86.285 2330 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.18 % Allowed : 20.12 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.22), residues: 1460 helix: -0.09 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 188 HIS 0.005 0.001 HIS A 399 PHE 0.015 0.001 PHE B 143 TYR 0.021 0.001 TYR D 391 ARG 0.004 0.001 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 325 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8299 (mt0) cc_final: 0.7894 (mp10) REVERT: A 122 THR cc_start: 0.8612 (m) cc_final: 0.8337 (m) REVERT: A 135 ILE cc_start: 0.7558 (tt) cc_final: 0.7345 (tt) REVERT: A 338 LEU cc_start: 0.7998 (tp) cc_final: 0.7784 (tp) REVERT: A 368 GLU cc_start: 0.8102 (tp30) cc_final: 0.7736 (tp30) REVERT: A 376 MET cc_start: 0.7971 (tpp) cc_final: 0.7727 (ttp) REVERT: A 442 LEU cc_start: 0.8200 (mt) cc_final: 0.7969 (mt) REVERT: A 444 PHE cc_start: 0.7988 (m-80) cc_final: 0.7208 (m-80) REVERT: A 449 MET cc_start: 0.8271 (ttt) cc_final: 0.8040 (ttt) REVERT: A 480 MET cc_start: 0.7876 (mmt) cc_final: 0.7318 (tmm) REVERT: B 169 THR cc_start: 0.8538 (t) cc_final: 0.8326 (p) REVERT: B 235 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8416 (mm-30) REVERT: B 247 LEU cc_start: 0.9289 (mm) cc_final: 0.8746 (tt) REVERT: B 281 ILE cc_start: 0.8456 (mm) cc_final: 0.8033 (tp) REVERT: B 283 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8193 (mmt90) REVERT: B 300 ASN cc_start: 0.7370 (m-40) cc_final: 0.6569 (t0) REVERT: B 350 MET cc_start: 0.7975 (mmm) cc_final: 0.7409 (mpp) REVERT: B 360 HIS cc_start: 0.7988 (t70) cc_final: 0.7469 (t70) REVERT: B 379 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7320 (mtp85) REVERT: B 380 ASP cc_start: 0.7368 (p0) cc_final: 0.6683 (p0) REVERT: B 393 THR cc_start: 0.8598 (p) cc_final: 0.8023 (t) REVERT: B 419 ARG cc_start: 0.5667 (ptt-90) cc_final: 0.4480 (ptm160) REVERT: B 473 TRP cc_start: 0.8015 (t-100) cc_final: 0.6864 (m-90) REVERT: C 122 THR cc_start: 0.8557 (m) cc_final: 0.8304 (m) REVERT: C 336 LEU cc_start: 0.9094 (mm) cc_final: 0.8831 (mm) REVERT: C 368 GLU cc_start: 0.8061 (tp30) cc_final: 0.7844 (tp30) REVERT: C 374 ASP cc_start: 0.7693 (t0) cc_final: 0.7437 (t0) REVERT: C 391 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7207 (t80) REVERT: C 444 PHE cc_start: 0.8037 (m-80) cc_final: 0.6945 (m-80) REVERT: C 495 GLU cc_start: 0.6343 (tt0) cc_final: 0.6103 (tp30) REVERT: D 115 MET cc_start: 0.8045 (tpt) cc_final: 0.7844 (tpt) REVERT: D 126 MET cc_start: 0.7551 (ttp) cc_final: 0.7333 (ttm) REVERT: D 170 TRP cc_start: 0.8187 (t60) cc_final: 0.6918 (t60) REVERT: D 201 CYS cc_start: 0.7676 (m) cc_final: 0.6816 (p) REVERT: D 247 LEU cc_start: 0.9152 (mm) cc_final: 0.8597 (tt) REVERT: D 380 ASP cc_start: 0.6703 (p0) cc_final: 0.5881 (p0) REVERT: D 391 TYR cc_start: 0.8036 (m-80) cc_final: 0.7659 (t80) REVERT: D 408 GLN cc_start: 0.8195 (mt0) cc_final: 0.7861 (mm-40) REVERT: D 473 TRP cc_start: 0.8038 (t-100) cc_final: 0.6954 (m-90) REVERT: D 476 LEU cc_start: 0.8250 (tt) cc_final: 0.7505 (mm) outliers start: 54 outliers final: 27 residues processed: 353 average time/residue: 0.2082 time to fit residues: 110.0964 Evaluate side-chains 312 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 217 HIS B 303 GLN B 434 HIS C 119 HIS C 474 ASN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 217 HIS D 300 ASN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13120 Z= 0.542 Angle : 0.941 11.505 17864 Z= 0.458 Chirality : 0.053 0.258 1984 Planarity : 0.006 0.048 2108 Dihedral : 8.704 60.896 2316 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 7.51 % Allowed : 23.14 % Favored : 69.35 % 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: -1.10 (0.21), residues: 1460 helix: -0.05 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -2.50 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 394 HIS 0.012 0.002 HIS C 399 PHE 0.030 0.003 PHE C 453 TYR 0.026 0.003 TYR A 291 ARG 0.007 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 296 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8435 (mt0) cc_final: 0.8064 (mp10) REVERT: A 122 THR cc_start: 0.8796 (m) cc_final: 0.8539 (m) REVERT: A 142 ASP cc_start: 0.7412 (m-30) cc_final: 0.7082 (m-30) REVERT: A 153 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 221 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7631 (tt0) REVERT: A 223 GLN cc_start: 0.6947 (mt0) cc_final: 0.6075 (pp30) REVERT: A 284 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 336 LEU cc_start: 0.9274 (mm) cc_final: 0.8925 (tt) REVERT: A 350 MET cc_start: 0.7046 (tpt) cc_final: 0.6747 (mmm) REVERT: A 376 MET cc_start: 0.8036 (tpp) cc_final: 0.7727 (tmm) REVERT: A 391 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 442 LEU cc_start: 0.8157 (mt) cc_final: 0.7921 (mt) REVERT: A 444 PHE cc_start: 0.8373 (m-80) cc_final: 0.7691 (m-80) REVERT: B 142 ASP cc_start: 0.6954 (m-30) cc_final: 0.6604 (t0) REVERT: B 224 LEU cc_start: 0.8497 (mm) cc_final: 0.7993 (mm) REVERT: B 235 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 247 LEU cc_start: 0.9297 (mm) cc_final: 0.8661 (tt) REVERT: B 281 ILE cc_start: 0.8749 (mm) cc_final: 0.8542 (mm) REVERT: B 283 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8158 (mmt90) REVERT: B 286 TYR cc_start: 0.5986 (m-80) cc_final: 0.5622 (m-80) REVERT: B 300 ASN cc_start: 0.7678 (m-40) cc_final: 0.6835 (t0) REVERT: B 350 MET cc_start: 0.8022 (mmm) cc_final: 0.7479 (mpp) REVERT: B 391 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: B 419 ARG cc_start: 0.5753 (ptt-90) cc_final: 0.4192 (ptm160) REVERT: B 473 TRP cc_start: 0.8067 (t-100) cc_final: 0.6904 (m-90) REVERT: B 492 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: B 495 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.3856 (mp0) REVERT: C 122 THR cc_start: 0.8698 (m) cc_final: 0.8435 (m) REVERT: C 223 GLN cc_start: 0.6939 (mt0) cc_final: 0.6124 (pp30) REVERT: C 336 LEU cc_start: 0.9317 (mm) cc_final: 0.8896 (tt) REVERT: C 350 MET cc_start: 0.6982 (tpt) cc_final: 0.6748 (mmm) REVERT: C 368 GLU cc_start: 0.8366 (tp30) cc_final: 0.8155 (tp30) REVERT: C 391 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7533 (t80) REVERT: C 411 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8796 (mp) REVERT: D 126 MET cc_start: 0.7461 (ttp) cc_final: 0.7206 (ttm) REVERT: D 142 ASP cc_start: 0.7369 (m-30) cc_final: 0.7151 (t0) REVERT: D 224 LEU cc_start: 0.8495 (mm) cc_final: 0.8054 (mm) REVERT: D 235 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8044 (tp30) REVERT: D 326 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.4916 (ppp) REVERT: D 391 TYR cc_start: 0.8167 (m-80) cc_final: 0.7683 (t80) REVERT: D 408 GLN cc_start: 0.8465 (mt0) cc_final: 0.7987 (mm110) REVERT: D 473 TRP cc_start: 0.8044 (t-100) cc_final: 0.6806 (m-90) REVERT: D 492 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: D 497 TYR cc_start: 0.8622 (m-10) cc_final: 0.8379 (m-10) outliers start: 97 outliers final: 63 residues processed: 353 average time/residue: 0.2013 time to fit residues: 106.9150 Evaluate side-chains 337 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 265 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13120 Z= 0.191 Angle : 0.691 10.381 17864 Z= 0.323 Chirality : 0.041 0.200 1984 Planarity : 0.005 0.046 2108 Dihedral : 7.512 50.647 2316 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.49 % Allowed : 28.17 % Favored : 67.34 % 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: -0.22 (0.22), residues: 1460 helix: 0.60 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.39 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 294 HIS 0.003 0.001 HIS B 217 PHE 0.015 0.001 PHE A 387 TYR 0.017 0.001 TYR B 182 ARG 0.004 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 298 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8437 (mt0) cc_final: 0.8081 (mp10) REVERT: A 122 THR cc_start: 0.8782 (m) cc_final: 0.8511 (m) REVERT: A 135 ILE cc_start: 0.7612 (tt) cc_final: 0.7408 (tt) REVERT: A 221 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7569 (tt0) REVERT: A 376 MET cc_start: 0.7978 (tpp) cc_final: 0.7760 (tmm) REVERT: A 444 PHE cc_start: 0.8303 (m-80) cc_final: 0.7625 (m-80) REVERT: B 101 GLN cc_start: 0.8286 (mt0) cc_final: 0.7342 (pp30) REVERT: B 142 ASP cc_start: 0.7020 (m-30) cc_final: 0.6671 (t0) REVERT: B 170 TRP cc_start: 0.8169 (t60) cc_final: 0.7156 (t60) REVERT: B 224 LEU cc_start: 0.8381 (mm) cc_final: 0.7968 (mm) REVERT: B 235 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 249 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8503 (mm-30) REVERT: B 281 ILE cc_start: 0.8828 (mm) cc_final: 0.8482 (mm) REVERT: B 286 TYR cc_start: 0.6035 (m-80) cc_final: 0.5715 (m-80) REVERT: B 300 ASN cc_start: 0.7151 (m-40) cc_final: 0.6497 (t0) REVERT: B 350 MET cc_start: 0.7958 (mmm) cc_final: 0.7416 (tpp) REVERT: B 391 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: B 419 ARG cc_start: 0.5536 (ptt-90) cc_final: 0.3926 (ptm160) REVERT: B 453 PHE cc_start: 0.7820 (t80) cc_final: 0.7464 (t80) REVERT: B 473 TRP cc_start: 0.8082 (t-100) cc_final: 0.6891 (m-90) REVERT: B 492 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: C 122 THR cc_start: 0.8630 (m) cc_final: 0.8348 (m) REVERT: C 153 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: C 221 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7611 (tt0) REVERT: C 286 TYR cc_start: 0.7954 (m-80) cc_final: 0.7519 (m-80) REVERT: C 368 GLU cc_start: 0.8162 (tp30) cc_final: 0.7944 (tp30) REVERT: C 374 ASP cc_start: 0.8445 (t70) cc_final: 0.7667 (t0) REVERT: C 444 PHE cc_start: 0.8354 (m-10) cc_final: 0.7794 (m-80) REVERT: C 492 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: D 126 MET cc_start: 0.7598 (ttp) cc_final: 0.7378 (ttm) REVERT: D 142 ASP cc_start: 0.7200 (m-30) cc_final: 0.6969 (t0) REVERT: D 224 LEU cc_start: 0.8422 (mm) cc_final: 0.7963 (mm) REVERT: D 235 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7930 (mm-30) REVERT: D 300 ASN cc_start: 0.6764 (t0) cc_final: 0.6261 (t0) REVERT: D 360 HIS cc_start: 0.7652 (t-90) cc_final: 0.7116 (t-170) REVERT: D 391 TYR cc_start: 0.8018 (m-80) cc_final: 0.7631 (t80) REVERT: D 408 GLN cc_start: 0.8373 (mt0) cc_final: 0.7944 (mm110) REVERT: D 419 ARG cc_start: 0.5383 (ptt-90) cc_final: 0.4337 (ptm160) REVERT: D 473 TRP cc_start: 0.8084 (t-100) cc_final: 0.6869 (m-90) REVERT: D 492 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8218 (m-80) outliers start: 58 outliers final: 40 residues processed: 331 average time/residue: 0.2111 time to fit residues: 104.5237 Evaluate side-chains 325 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 119 HIS B 217 HIS B 488 GLN C 461 ASN D 119 HIS D 217 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13120 Z= 0.173 Angle : 0.675 10.440 17864 Z= 0.311 Chirality : 0.040 0.178 1984 Planarity : 0.004 0.047 2108 Dihedral : 7.194 59.957 2316 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.11 % Allowed : 28.41 % Favored : 66.49 % 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: 0.08 (0.23), residues: 1460 helix: 0.92 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.56 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 478 HIS 0.004 0.001 HIS D 217 PHE 0.011 0.001 PHE B 104 TYR 0.019 0.001 TYR B 182 ARG 0.003 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 301 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8501 (mt0) cc_final: 0.8061 (mp10) REVERT: A 122 THR cc_start: 0.8694 (m) cc_final: 0.8398 (m) REVERT: A 221 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7542 (tt0) REVERT: A 286 TYR cc_start: 0.7850 (m-80) cc_final: 0.7537 (m-80) REVERT: A 444 PHE cc_start: 0.8251 (m-80) cc_final: 0.7652 (m-80) REVERT: B 101 GLN cc_start: 0.8078 (mt0) cc_final: 0.7193 (pp30) REVERT: B 142 ASP cc_start: 0.7012 (m-30) cc_final: 0.6766 (t0) REVERT: B 224 LEU cc_start: 0.8256 (mm) cc_final: 0.7894 (mm) REVERT: B 235 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 249 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8550 (mm-30) REVERT: B 281 ILE cc_start: 0.8758 (mm) cc_final: 0.8420 (mm) REVERT: B 283 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7581 (mmm160) REVERT: B 286 TYR cc_start: 0.6085 (m-80) cc_final: 0.5750 (m-10) REVERT: B 300 ASN cc_start: 0.7075 (m-40) cc_final: 0.6387 (t0) REVERT: B 350 MET cc_start: 0.7922 (mmm) cc_final: 0.7369 (tpp) REVERT: B 360 HIS cc_start: 0.7777 (t-90) cc_final: 0.7427 (t-170) REVERT: B 391 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: B 419 ARG cc_start: 0.5403 (ptt-90) cc_final: 0.3871 (ptm160) REVERT: B 453 PHE cc_start: 0.7872 (t80) cc_final: 0.7542 (t80) REVERT: B 473 TRP cc_start: 0.8101 (t-100) cc_final: 0.6900 (m-90) REVERT: B 492 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: C 122 THR cc_start: 0.8570 (m) cc_final: 0.8291 (m) REVERT: C 341 LEU cc_start: 0.7930 (tp) cc_final: 0.7444 (tp) REVERT: C 368 GLU cc_start: 0.8069 (tp30) cc_final: 0.7796 (tp30) REVERT: C 374 ASP cc_start: 0.8500 (t70) cc_final: 0.7684 (t0) REVERT: C 444 PHE cc_start: 0.8352 (m-10) cc_final: 0.7805 (m-80) REVERT: D 142 ASP cc_start: 0.7183 (m-30) cc_final: 0.6970 (t0) REVERT: D 170 TRP cc_start: 0.8208 (t60) cc_final: 0.7445 (t60) REVERT: D 224 LEU cc_start: 0.8336 (mm) cc_final: 0.7843 (mm) REVERT: D 235 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 300 ASN cc_start: 0.6755 (t0) cc_final: 0.6218 (t0) REVERT: D 326 MET cc_start: 0.5752 (tmm) cc_final: 0.5066 (ppp) REVERT: D 360 HIS cc_start: 0.7672 (t-90) cc_final: 0.7310 (t-90) REVERT: D 391 TYR cc_start: 0.7892 (m-80) cc_final: 0.7462 (t80) REVERT: D 408 GLN cc_start: 0.8273 (mt0) cc_final: 0.7914 (mm110) REVERT: D 419 ARG cc_start: 0.5111 (ptt-90) cc_final: 0.4040 (ptm160) REVERT: D 473 TRP cc_start: 0.8181 (t-100) cc_final: 0.6973 (m-90) REVERT: D 492 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: D 495 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4425 (mp0) REVERT: D 497 TYR cc_start: 0.8557 (m-10) cc_final: 0.8339 (m-10) outliers start: 66 outliers final: 48 residues processed: 343 average time/residue: 0.2294 time to fit residues: 118.0845 Evaluate side-chains 331 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 279 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 217 HIS C 383 ASN D 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13120 Z= 0.183 Angle : 0.681 10.578 17864 Z= 0.311 Chirality : 0.040 0.166 1984 Planarity : 0.004 0.046 2108 Dihedral : 6.821 57.567 2316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.88 % Allowed : 28.41 % Favored : 65.71 % 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: 0.09 (0.22), residues: 1460 helix: 0.95 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.73 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 478 HIS 0.004 0.001 HIS D 217 PHE 0.014 0.001 PHE A 387 TYR 0.016 0.001 TYR B 182 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8479 (mt0) cc_final: 0.8055 (mp10) REVERT: A 122 THR cc_start: 0.8713 (m) cc_final: 0.8430 (m) REVERT: A 188 TRP cc_start: 0.6498 (m-10) cc_final: 0.6288 (m-10) REVERT: A 444 PHE cc_start: 0.8265 (m-80) cc_final: 0.7276 (m-80) REVERT: A 449 MET cc_start: 0.8271 (tpp) cc_final: 0.7884 (tpp) REVERT: B 142 ASP cc_start: 0.7001 (m-30) cc_final: 0.6783 (t0) REVERT: B 224 LEU cc_start: 0.8267 (mm) cc_final: 0.7850 (mm) REVERT: B 281 ILE cc_start: 0.8733 (mm) cc_final: 0.8211 (tt) REVERT: B 300 ASN cc_start: 0.7104 (m-40) cc_final: 0.6519 (t0) REVERT: B 350 MET cc_start: 0.7877 (mmm) cc_final: 0.7587 (tpp) REVERT: B 360 HIS cc_start: 0.7782 (t-90) cc_final: 0.7443 (t-170) REVERT: B 368 GLU cc_start: 0.8397 (tp30) cc_final: 0.7902 (tp30) REVERT: B 391 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: B 408 GLN cc_start: 0.8285 (mt0) cc_final: 0.7693 (mm110) REVERT: B 419 ARG cc_start: 0.5262 (ptt-90) cc_final: 0.3776 (ptm160) REVERT: B 473 TRP cc_start: 0.8075 (t-100) cc_final: 0.6877 (m-90) REVERT: B 492 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 495 GLU cc_start: 0.4653 (OUTLIER) cc_final: 0.4142 (mp0) REVERT: C 122 THR cc_start: 0.8567 (m) cc_final: 0.8272 (m) REVERT: C 153 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: C 188 TRP cc_start: 0.6686 (m-10) cc_final: 0.6472 (m-10) REVERT: C 221 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7531 (tt0) REVERT: C 286 TYR cc_start: 0.7872 (m-80) cc_final: 0.7468 (m-80) REVERT: C 341 LEU cc_start: 0.8043 (tp) cc_final: 0.7613 (tp) REVERT: C 368 GLU cc_start: 0.8107 (tp30) cc_final: 0.7903 (tp30) REVERT: C 374 ASP cc_start: 0.8465 (t70) cc_final: 0.7609 (t0) REVERT: C 376 MET cc_start: 0.8124 (tpp) cc_final: 0.7711 (tmm) REVERT: C 444 PHE cc_start: 0.8355 (m-10) cc_final: 0.7838 (m-80) REVERT: C 492 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: C 495 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5867 (mm-30) REVERT: D 170 TRP cc_start: 0.8188 (t60) cc_final: 0.7970 (t60) REVERT: D 224 LEU cc_start: 0.8385 (mm) cc_final: 0.7784 (mm) REVERT: D 235 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 300 ASN cc_start: 0.6855 (t0) cc_final: 0.6257 (t0) REVERT: D 326 MET cc_start: 0.5929 (tmm) cc_final: 0.5138 (ppp) REVERT: D 360 HIS cc_start: 0.7713 (t-90) cc_final: 0.7472 (t-90) REVERT: D 408 GLN cc_start: 0.8214 (mt0) cc_final: 0.7876 (mm110) REVERT: D 419 ARG cc_start: 0.5028 (ptt-90) cc_final: 0.3932 (ptm160) REVERT: D 473 TRP cc_start: 0.8071 (t-100) cc_final: 0.6895 (m-90) REVERT: D 492 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: D 495 GLU cc_start: 0.4883 (OUTLIER) cc_final: 0.4370 (mp0) REVERT: D 497 TYR cc_start: 0.8587 (m-10) cc_final: 0.8382 (m-10) outliers start: 76 outliers final: 56 residues processed: 341 average time/residue: 0.2050 time to fit residues: 105.3196 Evaluate side-chains 342 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS D 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13120 Z= 0.188 Angle : 0.695 10.533 17864 Z= 0.319 Chirality : 0.040 0.146 1984 Planarity : 0.004 0.045 2108 Dihedral : 6.790 58.187 2316 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.19 % Allowed : 29.80 % Favored : 65.02 % 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: 0.12 (0.22), residues: 1460 helix: 0.98 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.81 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 478 HIS 0.003 0.001 HIS C 399 PHE 0.017 0.001 PHE B 239 TYR 0.018 0.001 TYR B 182 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 288 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8466 (mt0) cc_final: 0.8111 (mp10) REVERT: A 122 THR cc_start: 0.8702 (m) cc_final: 0.8408 (m) REVERT: A 375 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7544 (mtt-85) REVERT: A 444 PHE cc_start: 0.8416 (m-80) cc_final: 0.7746 (m-80) REVERT: B 142 ASP cc_start: 0.7011 (m-30) cc_final: 0.6782 (t0) REVERT: B 224 LEU cc_start: 0.8183 (mm) cc_final: 0.7824 (mm) REVERT: B 235 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6733 (mm-30) REVERT: B 238 ARG cc_start: 0.8787 (ptm-80) cc_final: 0.8566 (ptm-80) REVERT: B 281 ILE cc_start: 0.8817 (mm) cc_final: 0.8233 (tt) REVERT: B 300 ASN cc_start: 0.7181 (m-40) cc_final: 0.6493 (t0) REVERT: B 350 MET cc_start: 0.7886 (mmm) cc_final: 0.7557 (tpp) REVERT: B 360 HIS cc_start: 0.7783 (t-90) cc_final: 0.7473 (t-170) REVERT: B 408 GLN cc_start: 0.8236 (mt0) cc_final: 0.7733 (mm-40) REVERT: B 419 ARG cc_start: 0.5221 (ptt-90) cc_final: 0.3694 (ptm160) REVERT: B 473 TRP cc_start: 0.8033 (t-100) cc_final: 0.6917 (m-90) REVERT: B 492 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: B 495 GLU cc_start: 0.4696 (OUTLIER) cc_final: 0.4164 (mp0) REVERT: C 153 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: C 188 TRP cc_start: 0.6788 (m-10) cc_final: 0.6567 (m-10) REVERT: C 221 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7532 (tt0) REVERT: C 223 GLN cc_start: 0.6843 (mt0) cc_final: 0.6210 (tm-30) REVERT: C 286 TYR cc_start: 0.7881 (m-80) cc_final: 0.7568 (m-80) REVERT: C 374 ASP cc_start: 0.8495 (t70) cc_final: 0.7729 (t0) REVERT: C 376 MET cc_start: 0.8029 (tpp) cc_final: 0.7662 (tmm) REVERT: C 439 CYS cc_start: 0.8130 (t) cc_final: 0.7925 (m) REVERT: C 444 PHE cc_start: 0.8417 (m-10) cc_final: 0.7505 (m-80) REVERT: C 495 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5977 (mm-30) REVERT: D 170 TRP cc_start: 0.8200 (t60) cc_final: 0.7985 (t60) REVERT: D 224 LEU cc_start: 0.8226 (mm) cc_final: 0.7811 (mm) REVERT: D 300 ASN cc_start: 0.6900 (t0) cc_final: 0.6313 (t0) REVERT: D 408 GLN cc_start: 0.8203 (mt0) cc_final: 0.7841 (mm110) REVERT: D 473 TRP cc_start: 0.8041 (t-100) cc_final: 0.6892 (m-90) REVERT: D 492 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: D 495 GLU cc_start: 0.5006 (OUTLIER) cc_final: 0.4497 (mp0) outliers start: 67 outliers final: 48 residues processed: 334 average time/residue: 0.1974 time to fit residues: 100.7799 Evaluate side-chains 330 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 277 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS D 217 HIS D 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13120 Z= 0.182 Angle : 0.702 11.726 17864 Z= 0.322 Chirality : 0.040 0.141 1984 Planarity : 0.004 0.045 2108 Dihedral : 6.679 59.445 2316 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.95 % Allowed : 29.64 % Favored : 65.40 % 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: 0.21 (0.22), residues: 1460 helix: 1.04 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 478 HIS 0.003 0.001 HIS C 399 PHE 0.016 0.001 PHE A 372 TYR 0.018 0.001 TYR D 182 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 275 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8402 (mt0) cc_final: 0.8096 (mp10) REVERT: A 122 THR cc_start: 0.8737 (m) cc_final: 0.8450 (m) REVERT: A 223 GLN cc_start: 0.7746 (tp40) cc_final: 0.6818 (pp30) REVERT: A 375 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7715 (mtt-85) REVERT: A 444 PHE cc_start: 0.8421 (m-80) cc_final: 0.7897 (m-80) REVERT: B 173 MET cc_start: 0.9295 (ppp) cc_final: 0.8964 (ppp) REVERT: B 249 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8439 (mm-30) REVERT: B 281 ILE cc_start: 0.8786 (mm) cc_final: 0.8495 (mm) REVERT: B 300 ASN cc_start: 0.7126 (m-40) cc_final: 0.6453 (t0) REVERT: B 350 MET cc_start: 0.7843 (mmm) cc_final: 0.7391 (tpp) REVERT: B 360 HIS cc_start: 0.7846 (t-90) cc_final: 0.7509 (t-90) REVERT: B 408 GLN cc_start: 0.8191 (mt0) cc_final: 0.7700 (mm-40) REVERT: B 449 MET cc_start: 0.5736 (ttt) cc_final: 0.5497 (tpt) REVERT: B 473 TRP cc_start: 0.8002 (t-100) cc_final: 0.6883 (m-90) REVERT: B 492 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: B 495 GLU cc_start: 0.4739 (OUTLIER) cc_final: 0.4182 (mp0) REVERT: C 142 ASP cc_start: 0.6660 (m-30) cc_final: 0.6436 (m-30) REVERT: C 152 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6276 (mm-30) REVERT: C 188 TRP cc_start: 0.6898 (m-10) cc_final: 0.6682 (m-10) REVERT: C 221 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7486 (tt0) REVERT: C 223 GLN cc_start: 0.6797 (mt0) cc_final: 0.6147 (tm-30) REVERT: C 286 TYR cc_start: 0.7826 (m-80) cc_final: 0.7603 (m-80) REVERT: C 368 GLU cc_start: 0.7827 (tp30) cc_final: 0.7401 (tp30) REVERT: C 374 ASP cc_start: 0.8459 (t70) cc_final: 0.7749 (t0) REVERT: C 376 MET cc_start: 0.8137 (tpp) cc_final: 0.7716 (tmm) REVERT: C 444 PHE cc_start: 0.8402 (m-10) cc_final: 0.7487 (m-80) REVERT: C 495 GLU cc_start: 0.6462 (mm-30) cc_final: 0.6229 (mm-30) REVERT: D 142 ASP cc_start: 0.7810 (t0) cc_final: 0.7604 (t0) REVERT: D 224 LEU cc_start: 0.8353 (mm) cc_final: 0.7836 (mm) REVERT: D 300 ASN cc_start: 0.6786 (t0) cc_final: 0.6247 (t0) REVERT: D 408 GLN cc_start: 0.8183 (mt0) cc_final: 0.7810 (mm110) REVERT: D 453 PHE cc_start: 0.7560 (t80) cc_final: 0.7298 (t80) REVERT: D 473 TRP cc_start: 0.8071 (t-100) cc_final: 0.6899 (m-90) REVERT: D 495 GLU cc_start: 0.5039 (OUTLIER) cc_final: 0.4521 (mp0) outliers start: 64 outliers final: 54 residues processed: 316 average time/residue: 0.1938 time to fit residues: 94.2365 Evaluate side-chains 318 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 236 GLN B 217 HIS B 223 GLN C 222 HIS D 217 HIS D 222 HIS D 223 GLN D 485 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 13120 Z= 0.566 Angle : 0.961 13.008 17864 Z= 0.462 Chirality : 0.052 0.246 1984 Planarity : 0.006 0.045 2108 Dihedral : 7.659 58.732 2316 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.27 % Allowed : 29.33 % Favored : 64.40 % 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: -0.60 (0.21), residues: 1460 helix: 0.40 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 478 HIS 0.025 0.003 HIS B 217 PHE 0.025 0.003 PHE A 366 TYR 0.030 0.002 TYR C 407 ARG 0.006 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 268 time to evaluate : 1.240 Fit side-chains REVERT: A 101 GLN cc_start: 0.8538 (mt0) cc_final: 0.8168 (mp10) REVERT: A 115 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.6586 (mpm) REVERT: A 142 ASP cc_start: 0.7245 (m-30) cc_final: 0.7026 (m-30) REVERT: A 223 GLN cc_start: 0.7960 (tp40) cc_final: 0.7294 (pp30) REVERT: A 336 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8880 (tt) REVERT: A 400 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8154 (t0) REVERT: A 444 PHE cc_start: 0.8615 (m-80) cc_final: 0.7981 (m-80) REVERT: B 142 ASP cc_start: 0.7495 (m-30) cc_final: 0.7191 (t0) REVERT: B 224 LEU cc_start: 0.8478 (mm) cc_final: 0.8231 (mm) REVERT: B 249 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8364 (mm-30) REVERT: B 281 ILE cc_start: 0.8823 (mm) cc_final: 0.8407 (tp) REVERT: B 300 ASN cc_start: 0.7685 (m-40) cc_final: 0.6868 (t0) REVERT: B 326 MET cc_start: 0.4276 (tpt) cc_final: 0.4071 (tpt) REVERT: B 350 MET cc_start: 0.8054 (mmm) cc_final: 0.7783 (tpp) REVERT: B 408 GLN cc_start: 0.8354 (mt0) cc_final: 0.7778 (mm110) REVERT: B 419 ARG cc_start: 0.5529 (ptt-90) cc_final: 0.4048 (ptm160) REVERT: B 492 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: B 495 GLU cc_start: 0.4699 (OUTLIER) cc_final: 0.4048 (mp0) REVERT: C 153 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: C 221 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7718 (tt0) REVERT: C 223 GLN cc_start: 0.7081 (mt0) cc_final: 0.6280 (pp30) REVERT: C 286 TYR cc_start: 0.8303 (m-80) cc_final: 0.7812 (m-80) REVERT: C 336 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 376 MET cc_start: 0.8201 (tpp) cc_final: 0.7643 (tmm) REVERT: C 411 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8700 (mp) REVERT: C 444 PHE cc_start: 0.8554 (m-10) cc_final: 0.8008 (m-80) REVERT: C 495 GLU cc_start: 0.6297 (mm-30) cc_final: 0.5970 (mm-30) REVERT: D 224 LEU cc_start: 0.8538 (mm) cc_final: 0.8068 (mm) REVERT: D 238 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8549 (ptm-80) REVERT: D 300 ASN cc_start: 0.7526 (t0) cc_final: 0.6886 (t0) REVERT: D 408 GLN cc_start: 0.8402 (mt0) cc_final: 0.7948 (mm-40) REVERT: D 419 ARG cc_start: 0.5416 (ptt-90) cc_final: 0.3885 (ptm160) REVERT: D 492 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: D 495 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4420 (mp0) outliers start: 81 outliers final: 53 residues processed: 321 average time/residue: 0.2108 time to fit residues: 103.5070 Evaluate side-chains 316 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 253 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS B 223 GLN B 488 GLN D 217 HIS D 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13120 Z= 0.211 Angle : 0.768 11.141 17864 Z= 0.355 Chirality : 0.042 0.197 1984 Planarity : 0.005 0.047 2108 Dihedral : 7.056 59.714 2316 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.33 % Allowed : 31.81 % Favored : 63.85 % 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: -0.19 (0.22), residues: 1460 helix: 0.67 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.65 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 478 HIS 0.004 0.001 HIS A 399 PHE 0.012 0.001 PHE A 372 TYR 0.025 0.001 TYR C 407 ARG 0.005 0.000 ARG B 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8467 (mt0) cc_final: 0.8087 (mp10) REVERT: A 223 GLN cc_start: 0.7891 (tp40) cc_final: 0.7289 (pp30) REVERT: A 374 ASP cc_start: 0.8333 (t70) cc_final: 0.7539 (t0) REVERT: B 102 LYS cc_start: 0.6937 (pptt) cc_final: 0.6428 (tptp) REVERT: B 142 ASP cc_start: 0.7511 (m-30) cc_final: 0.7259 (t0) REVERT: B 173 MET cc_start: 0.9274 (ppp) cc_final: 0.9044 (ppp) REVERT: B 224 LEU cc_start: 0.8357 (mm) cc_final: 0.8049 (mm) REVERT: B 241 MET cc_start: 0.8190 (mtt) cc_final: 0.7710 (mmt) REVERT: B 281 ILE cc_start: 0.8810 (mm) cc_final: 0.8462 (pt) REVERT: B 300 ASN cc_start: 0.7218 (m-40) cc_final: 0.6545 (t0) REVERT: B 350 MET cc_start: 0.8047 (mmm) cc_final: 0.7473 (tpp) REVERT: B 360 HIS cc_start: 0.7860 (t-90) cc_final: 0.7445 (t-170) REVERT: B 376 MET cc_start: 0.7324 (tpt) cc_final: 0.6109 (tmm) REVERT: B 419 ARG cc_start: 0.5378 (ptt-90) cc_final: 0.3802 (ptm160) REVERT: B 492 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: B 495 GLU cc_start: 0.4543 (OUTLIER) cc_final: 0.3916 (mp0) REVERT: C 153 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: C 221 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7602 (tt0) REVERT: C 286 TYR cc_start: 0.7778 (m-80) cc_final: 0.7484 (m-80) REVERT: C 368 GLU cc_start: 0.7890 (tp30) cc_final: 0.7638 (tp30) REVERT: C 374 ASP cc_start: 0.8351 (t70) cc_final: 0.7672 (t0) REVERT: C 376 MET cc_start: 0.8185 (tpp) cc_final: 0.7817 (tmm) REVERT: C 444 PHE cc_start: 0.8457 (m-10) cc_final: 0.7877 (m-80) REVERT: C 495 GLU cc_start: 0.6333 (mm-30) cc_final: 0.6037 (mm-30) REVERT: D 170 TRP cc_start: 0.8160 (t60) cc_final: 0.7860 (t60) REVERT: D 207 HIS cc_start: 0.8853 (t-90) cc_final: 0.8626 (t-90) REVERT: D 224 LEU cc_start: 0.8417 (mm) cc_final: 0.7966 (mm) REVERT: D 238 ARG cc_start: 0.8821 (ptm-80) cc_final: 0.8537 (ptm-80) REVERT: D 300 ASN cc_start: 0.6926 (t0) cc_final: 0.6376 (t0) REVERT: D 408 GLN cc_start: 0.8294 (mt0) cc_final: 0.7832 (mm-40) REVERT: D 419 ARG cc_start: 0.5252 (ptt-90) cc_final: 0.3752 (ptm160) REVERT: D 473 TRP cc_start: 0.8016 (t-100) cc_final: 0.6879 (m-90) REVERT: D 495 GLU cc_start: 0.4777 (OUTLIER) cc_final: 0.4308 (mp0) outliers start: 56 outliers final: 46 residues processed: 301 average time/residue: 0.2019 time to fit residues: 92.4489 Evaluate side-chains 308 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 258 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 488 GLN Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 217 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN D 223 GLN ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116846 restraints weight = 22158.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119443 restraints weight = 12842.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121157 restraints weight = 9038.854| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 13120 Z= 0.380 Angle : 1.271 59.153 17864 Z= 0.740 Chirality : 0.075 2.627 1984 Planarity : 0.009 0.241 2108 Dihedral : 7.083 59.727 2316 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 4.18 % Allowed : 32.74 % Favored : 63.08 % Cbeta Deviations : 0.28 % 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: -0.21 (0.22), residues: 1460 helix: 0.64 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.63 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 478 HIS 0.384 0.013 HIS B 217 PHE 0.021 0.001 PHE A 444 TYR 0.030 0.002 TYR A 436 ARG 0.003 0.000 ARG B 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2708.50 seconds wall clock time: 49 minutes 19.01 seconds (2959.01 seconds total)