Starting phenix.real_space_refine on Thu Feb 15 02:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9i_30312/02_2024/7c9i_30312_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 7123 2.51 5 N 1709 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'FTO': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.13, per 1000 atoms: 0.56 Number of scatterers: 10853 At special positions: 0 Unit cell: (110.191, 93.826, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1979 8.00 N 1709 7.00 C 7123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.1 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 50.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.722A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.511A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.581A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.924A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 239 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.770A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.837A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.917A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.612A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 31 through 60 removed outlier: 3.892A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 102 removed outlier: 3.878A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 138 removed outlier: 3.861A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.767A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.111A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.550A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 48 through 81 removed outlier: 3.975A pdb=" N SER D 51 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 52 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 53 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 57 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 59 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 60 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 61 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 68 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 72 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 80 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 81 " --> pdb=" O PHE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.596A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.160A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.262A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 488 hydrogen bonds defined for protein. 1392 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: 2.95 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1639 1.31 - 1.44: 3156 1.44 - 1.56: 6269 1.56 - 1.69: 8 1.69 - 1.81: 61 Bond restraints: 11133 Sorted by residual: bond pdb=" C16 FTO B 502 " pdb=" N17 FTO B 502 " ideal model delta sigma weight residual 1.337 1.451 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C13 FTO B 502 " pdb=" N14 FTO B 502 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C10 FTO B 502 " pdb=" N11 FTO B 502 " ideal model delta sigma weight residual 1.347 1.452 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C04 FTO B 502 " pdb=" N05 FTO B 502 " ideal model delta sigma weight residual 1.350 1.452 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C04 FTO B 502 " pdb=" O03 FTO B 502 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 11128 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.25: 298 106.25 - 113.22: 6149 113.22 - 120.19: 4251 120.19 - 127.16: 4344 127.16 - 134.13: 143 Bond angle restraints: 15185 Sorted by residual: angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 131.19 -9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C PHE B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.33 124.40 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 131.78 -15.48 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 115.79 -5.09 1.22e+00 6.72e-01 1.74e+01 angle pdb=" N ALA A 157 " pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 110.97 115.28 -4.31 1.09e+00 8.42e-01 1.56e+01 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6625 22.70 - 45.40: 197 45.40 - 68.10: 49 68.10 - 90.80: 24 90.80 - 113.51: 18 Dihedral angle restraints: 6913 sinusoidal: 3080 harmonic: 3833 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -167.45 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -142.30 -37.70 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 145.95 -52.95 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1628 0.096 - 0.191: 168 0.191 - 0.287: 12 0.287 - 0.383: 4 0.383 - 0.478: 1 Chirality restraints: 1813 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 1810 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.027 2.00e-02 2.50e+03 2.11e-02 1.12e+01 pdb=" CG TRP C 227 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.024 2.00e-02 2.50e+03 1.83e-02 8.37e+00 pdb=" CG TRP D 36 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO A 560 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.041 5.00e-02 4.00e+02 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1902 2.77 - 3.30: 9707 3.30 - 3.83: 17458 3.83 - 4.37: 20879 4.37 - 4.90: 36562 Nonbonded interactions: 86508 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.232 2.440 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.240 2.440 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.282 2.440 nonbonded pdb=" OG SER D 7 " pdb=" OE1 GLU D 9 " model vdw 2.293 2.440 nonbonded pdb=" O GLU D 40 " pdb=" OH TYR D 47 " model vdw 2.303 2.440 ... (remaining 86503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 7.540 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.008 0.114 11133 Z= 0.496 Angle : 1.065 15.481 15185 Z= 0.544 Chirality : 0.062 0.478 1813 Planarity : 0.008 0.071 1833 Dihedral : 14.169 113.506 4431 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1303 helix: -2.14 (0.15), residues: 702 sheet: -1.99 (0.40), residues: 125 loop : -3.33 (0.22), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 227 HIS 0.026 0.003 HIS C 197 PHE 0.038 0.004 PHE C 132 TYR 0.038 0.003 TYR A 565 ARG 0.010 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.172 Fit side-chains REVERT: A 246 ILE cc_start: 0.8339 (mm) cc_final: 0.8096 (mt) REVERT: A 693 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8549 (mmtp) REVERT: B 165 TRP cc_start: 0.7283 (t60) cc_final: 0.6738 (t60) REVERT: B 169 SER cc_start: 0.9116 (t) cc_final: 0.8475 (p) REVERT: C 237 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6781 (mtt-85) REVERT: D 54 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6874 (ttpp) REVERT: D 91 TYR cc_start: 0.7591 (m-80) cc_final: 0.6970 (m-80) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.2454 time to fit residues: 65.7045 Evaluate side-chains 132 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN A 222 HIS A 355 GLN A 454 GLN A 531 ASN A 606 GLN B 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11133 Z= 0.197 Angle : 0.637 11.647 15185 Z= 0.309 Chirality : 0.044 0.252 1813 Planarity : 0.005 0.040 1833 Dihedral : 12.851 115.433 2127 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.24 % Allowed : 6.48 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1303 helix: -0.33 (0.19), residues: 708 sheet: -1.71 (0.40), residues: 122 loop : -2.78 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 209 HIS 0.009 0.001 HIS C 197 PHE 0.027 0.002 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.004 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.955 Fit side-chains REVERT: A 237 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7381 (mm-40) REVERT: A 693 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8565 (mmtp) REVERT: B 80 LYS cc_start: 0.8291 (tttt) cc_final: 0.7944 (tppt) REVERT: B 165 TRP cc_start: 0.7200 (t60) cc_final: 0.6640 (t60) REVERT: B 169 SER cc_start: 0.9088 (t) cc_final: 0.8486 (p) REVERT: C 140 ASP cc_start: 0.8268 (m-30) cc_final: 0.8056 (m-30) REVERT: D 34 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7920 (mp) REVERT: D 91 TYR cc_start: 0.7582 (m-80) cc_final: 0.6973 (m-80) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 0.2586 time to fit residues: 52.9832 Evaluate side-chains 131 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11133 Z= 0.200 Angle : 0.590 12.236 15185 Z= 0.286 Chirality : 0.043 0.241 1813 Planarity : 0.004 0.045 1833 Dihedral : 10.332 113.822 2123 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.87 % Allowed : 8.17 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1303 helix: 0.43 (0.20), residues: 712 sheet: -1.56 (0.41), residues: 126 loop : -2.51 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.027 0.002 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.240 Fit side-chains REVERT: A 237 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7536 (mm-40) REVERT: A 343 MET cc_start: 0.8181 (tpp) cc_final: 0.7741 (tpp) REVERT: A 693 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8583 (mmtp) REVERT: A 699 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7478 (pp) REVERT: B 80 LYS cc_start: 0.8250 (tttt) cc_final: 0.7929 (tppt) REVERT: B 165 TRP cc_start: 0.7244 (t60) cc_final: 0.6931 (t60) REVERT: B 169 SER cc_start: 0.9088 (t) cc_final: 0.8485 (p) REVERT: B 210 MET cc_start: 0.8574 (mmt) cc_final: 0.7942 (mmt) REVERT: C 140 ASP cc_start: 0.8391 (m-30) cc_final: 0.8186 (m-30) REVERT: D 34 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8037 (mp) REVERT: D 91 TYR cc_start: 0.7553 (m-80) cc_final: 0.6888 (m-80) outliers start: 21 outliers final: 12 residues processed: 141 average time/residue: 0.2609 time to fit residues: 51.2036 Evaluate side-chains 128 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11133 Z= 0.171 Angle : 0.558 11.249 15185 Z= 0.269 Chirality : 0.042 0.242 1813 Planarity : 0.004 0.040 1833 Dihedral : 9.601 113.340 2123 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.69 % Allowed : 9.59 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.23), residues: 1303 helix: 0.83 (0.20), residues: 715 sheet: -1.40 (0.43), residues: 121 loop : -2.35 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.004 0.001 HIS C 197 PHE 0.025 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.007 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.103 Fit side-chains REVERT: A 138 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8811 (m) REVERT: A 143 ASP cc_start: 0.7855 (t0) cc_final: 0.7616 (t0) REVERT: A 215 MET cc_start: 0.8825 (ttm) cc_final: 0.8434 (ttp) REVERT: A 237 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7528 (mm-40) REVERT: A 343 MET cc_start: 0.8188 (tpp) cc_final: 0.7786 (tpp) REVERT: A 693 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8577 (mmtp) REVERT: A 699 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7477 (pp) REVERT: B 80 LYS cc_start: 0.8231 (tttt) cc_final: 0.7923 (tppt) REVERT: B 165 TRP cc_start: 0.7167 (t60) cc_final: 0.6840 (t60) REVERT: B 169 SER cc_start: 0.9080 (t) cc_final: 0.8482 (p) REVERT: B 210 MET cc_start: 0.8605 (mmt) cc_final: 0.7893 (mmt) REVERT: C 138 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 140 ASP cc_start: 0.8387 (m-30) cc_final: 0.8167 (m-30) REVERT: D 91 TYR cc_start: 0.7474 (m-80) cc_final: 0.6893 (m-80) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.2528 time to fit residues: 46.3234 Evaluate side-chains 125 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 51 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.0030 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11133 Z= 0.317 Angle : 0.655 13.292 15185 Z= 0.314 Chirality : 0.046 0.242 1813 Planarity : 0.004 0.069 1833 Dihedral : 9.637 97.133 2123 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.22 % Allowed : 10.30 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.23), residues: 1303 helix: 0.80 (0.20), residues: 717 sheet: -1.33 (0.41), residues: 132 loop : -2.42 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.006 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.882 Fit side-chains REVERT: A 138 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8828 (m) REVERT: A 343 MET cc_start: 0.8206 (tpp) cc_final: 0.7880 (tpp) REVERT: A 699 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7512 (pp) REVERT: B 80 LYS cc_start: 0.8282 (tttt) cc_final: 0.7975 (tppt) REVERT: B 156 TYR cc_start: 0.4647 (m-80) cc_final: 0.4339 (m-80) REVERT: B 169 SER cc_start: 0.9091 (t) cc_final: 0.8433 (p) REVERT: B 210 MET cc_start: 0.8607 (mmt) cc_final: 0.7856 (mmt) REVERT: C 138 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8226 (mp) REVERT: C 140 ASP cc_start: 0.8403 (m-30) cc_final: 0.8192 (m-30) REVERT: D 91 TYR cc_start: 0.7450 (m-80) cc_final: 0.6809 (m-80) outliers start: 25 outliers final: 16 residues processed: 136 average time/residue: 0.2049 time to fit residues: 39.4997 Evaluate side-chains 136 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11133 Z= 0.280 Angle : 0.624 12.704 15185 Z= 0.301 Chirality : 0.044 0.239 1813 Planarity : 0.004 0.053 1833 Dihedral : 9.320 78.534 2123 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.95 % Allowed : 11.72 % Favored : 86.32 % 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: -0.67 (0.23), residues: 1303 helix: 0.91 (0.20), residues: 716 sheet: -1.34 (0.41), residues: 132 loop : -2.39 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.005 0.001 HIS C 197 PHE 0.029 0.002 PHE A 302 TYR 0.015 0.002 TYR A 569 ARG 0.007 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.304 Fit side-chains REVERT: A 138 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8828 (m) REVERT: A 343 MET cc_start: 0.8197 (tpp) cc_final: 0.7825 (tpp) REVERT: A 699 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7521 (pp) REVERT: B 80 LYS cc_start: 0.8214 (tttt) cc_final: 0.7903 (tppt) REVERT: B 169 SER cc_start: 0.9050 (t) cc_final: 0.8433 (p) REVERT: B 210 MET cc_start: 0.8594 (mmt) cc_final: 0.7853 (mmt) REVERT: C 140 ASP cc_start: 0.8393 (m-30) cc_final: 0.8184 (m-30) REVERT: D 91 TYR cc_start: 0.7453 (m-80) cc_final: 0.6778 (m-80) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.2506 time to fit residues: 47.6015 Evaluate side-chains 131 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11133 Z= 0.244 Angle : 0.607 12.207 15185 Z= 0.292 Chirality : 0.044 0.240 1813 Planarity : 0.004 0.045 1833 Dihedral : 8.935 77.539 2123 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 12.70 % Favored : 85.08 % 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: -0.57 (0.23), residues: 1303 helix: 0.99 (0.20), residues: 717 sheet: -1.27 (0.41), residues: 132 loop : -2.38 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.004 0.001 HIS C 197 PHE 0.027 0.002 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.007 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.189 Fit side-chains REVERT: A 138 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8828 (m) REVERT: A 343 MET cc_start: 0.8193 (tpp) cc_final: 0.7811 (tpp) REVERT: A 699 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7543 (pp) REVERT: B 80 LYS cc_start: 0.8278 (tttt) cc_final: 0.7982 (tppt) REVERT: B 169 SER cc_start: 0.9031 (t) cc_final: 0.8427 (p) REVERT: B 210 MET cc_start: 0.8580 (mmt) cc_final: 0.7867 (mmt) REVERT: C 140 ASP cc_start: 0.8389 (m-30) cc_final: 0.8186 (m-30) REVERT: D 91 TYR cc_start: 0.7486 (m-80) cc_final: 0.6784 (m-80) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.2535 time to fit residues: 46.1454 Evaluate side-chains 128 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11133 Z= 0.389 Angle : 0.697 13.649 15185 Z= 0.334 Chirality : 0.047 0.239 1813 Planarity : 0.005 0.045 1833 Dihedral : 9.233 78.052 2123 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.13 % Allowed : 13.06 % Favored : 84.81 % 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: -0.77 (0.23), residues: 1303 helix: 0.84 (0.20), residues: 717 sheet: -1.37 (0.41), residues: 132 loop : -2.48 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.006 0.002 HIS A 449 PHE 0.032 0.002 PHE A 302 TYR 0.017 0.002 TYR A 569 ARG 0.006 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.249 Fit side-chains REVERT: A 138 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 343 MET cc_start: 0.8185 (tpp) cc_final: 0.7911 (tpp) REVERT: A 699 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 80 LYS cc_start: 0.8230 (tttt) cc_final: 0.7889 (tppt) REVERT: B 169 SER cc_start: 0.9075 (t) cc_final: 0.8389 (p) REVERT: B 210 MET cc_start: 0.8574 (mmt) cc_final: 0.7895 (mmt) REVERT: C 140 ASP cc_start: 0.8373 (m-30) cc_final: 0.8154 (m-30) REVERT: D 81 TYR cc_start: 0.8005 (m-10) cc_final: 0.7709 (m-80) outliers start: 24 outliers final: 21 residues processed: 131 average time/residue: 0.2438 time to fit residues: 44.7363 Evaluate side-chains 134 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11133 Z= 0.351 Angle : 0.675 13.243 15185 Z= 0.324 Chirality : 0.046 0.237 1813 Planarity : 0.004 0.040 1833 Dihedral : 9.041 76.217 2123 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.40 % Allowed : 12.97 % Favored : 84.64 % 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: -0.77 (0.23), residues: 1303 helix: 0.83 (0.20), residues: 717 sheet: -1.35 (0.40), residues: 132 loop : -2.47 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 257 HIS 0.005 0.001 HIS A 449 PHE 0.031 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.006 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.173 Fit side-chains REVERT: A 138 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 343 MET cc_start: 0.8223 (tpp) cc_final: 0.7881 (tpp) REVERT: A 699 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7551 (pp) REVERT: B 80 LYS cc_start: 0.8327 (tttt) cc_final: 0.7957 (tppt) REVERT: B 169 SER cc_start: 0.9053 (t) cc_final: 0.8413 (p) REVERT: B 210 MET cc_start: 0.8570 (mmt) cc_final: 0.7859 (mmt) REVERT: C 140 ASP cc_start: 0.8383 (m-30) cc_final: 0.8183 (m-30) REVERT: D 8 ASN cc_start: 0.7537 (m110) cc_final: 0.7151 (m-40) REVERT: D 81 TYR cc_start: 0.8090 (m-10) cc_final: 0.7751 (m-80) REVERT: D 91 TYR cc_start: 0.7416 (m-80) cc_final: 0.6537 (m-80) outliers start: 27 outliers final: 21 residues processed: 133 average time/residue: 0.2493 time to fit residues: 46.6353 Evaluate side-chains 135 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11133 Z= 0.326 Angle : 0.665 13.159 15185 Z= 0.320 Chirality : 0.046 0.238 1813 Planarity : 0.004 0.041 1833 Dihedral : 8.883 75.629 2123 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.31 % Allowed : 13.14 % Favored : 84.55 % 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: -0.73 (0.23), residues: 1303 helix: 0.87 (0.20), residues: 717 sheet: -1.32 (0.40), residues: 133 loop : -2.46 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.005 0.001 HIS A 449 PHE 0.030 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.006 0.001 ARG C 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.921 Fit side-chains REVERT: A 138 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8869 (m) REVERT: A 343 MET cc_start: 0.8224 (tpp) cc_final: 0.7878 (tpp) REVERT: A 699 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7578 (pp) REVERT: B 80 LYS cc_start: 0.8198 (tttt) cc_final: 0.7817 (tppt) REVERT: B 169 SER cc_start: 0.9054 (t) cc_final: 0.8416 (p) REVERT: B 210 MET cc_start: 0.8571 (mmt) cc_final: 0.7872 (mmt) REVERT: D 8 ASN cc_start: 0.7585 (m110) cc_final: 0.7201 (m-40) REVERT: D 81 TYR cc_start: 0.8093 (m-10) cc_final: 0.7754 (m-80) REVERT: D 91 TYR cc_start: 0.7402 (m-80) cc_final: 0.6500 (m-80) outliers start: 26 outliers final: 23 residues processed: 133 average time/residue: 0.2099 time to fit residues: 39.4167 Evaluate side-chains 137 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 135 ASN D 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100606 restraints weight = 13900.955| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.92 r_work: 0.2937 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11133 Z= 0.186 Angle : 0.577 11.322 15185 Z= 0.279 Chirality : 0.042 0.241 1813 Planarity : 0.004 0.037 1833 Dihedral : 8.195 73.281 2123 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.04 % Allowed : 13.23 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.24), residues: 1303 helix: 1.07 (0.20), residues: 721 sheet: -1.15 (0.41), residues: 133 loop : -2.35 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.003 0.001 HIS A 553 PHE 0.026 0.001 PHE D 66 TYR 0.014 0.001 TYR A 569 ARG 0.006 0.000 ARG C 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.45 seconds wall clock time: 54 minutes 28.01 seconds (3268.01 seconds total)