Starting phenix.real_space_refine on Thu Feb 15 00:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8im7_35572/02_2024/8im7_35572_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.008 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 38 5.16 5 C 6941 2.51 5 N 1669 2.21 5 O 1937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10587 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: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2247 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.26, per 1000 atoms: 0.59 Number of scatterers: 10587 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 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 38 16.00 P 2 15.00 O 1937 8.00 N 1669 7.00 C 6941 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: 4.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 5 sheets defined 51.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 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 79 through 86 removed outlier: 3.660A pdb=" N TRP A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' 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 187 through 199 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 299 through 313 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 405 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.983A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.756A 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 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' 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 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.537A pdb=" N MET B 139 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.622A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 220 through 239 Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.646A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.941A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 removed outlier: 3.872A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.928A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.948A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 29 through 60 removed outlier: 4.265A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 102 removed outlier: 3.857A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 134 removed outlier: 3.606A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 183 removed outlier: 3.692A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 205 removed outlier: 4.558A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' 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 22 removed outlier: 3.900A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 removed outlier: 3.933A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) 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 80 removed outlier: 4.370A pdb=" N SER D 51 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG D 59 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 72 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 77 " --> pdb=" O TRP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.822A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 630 removed outlier: 4.191A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 281 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.504A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 474 hydrogen bonds defined for protein. 1326 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: 3.25 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 3002 1.45 - 1.57: 6043 1.57 - 1.69: 6 1.69 - 1.82: 58 Bond restraints: 10858 Sorted by residual: bond pdb=" N LEU B 435 " pdb=" CA LEU B 435 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.44e+01 bond pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.417 1.479 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 ... (remaining 10853 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.91: 241 105.91 - 113.68: 6340 113.68 - 121.45: 5851 121.45 - 129.22: 2282 129.22 - 136.99: 92 Bond angle restraints: 14806 Sorted by residual: angle pdb=" N LYS B 80 " pdb=" CA LYS B 80 " pdb=" C LYS B 80 " ideal model delta sigma weight residual 113.97 108.11 5.86 1.28e+00 6.10e-01 2.10e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.81 119.23 -9.42 2.21e+00 2.05e-01 1.82e+01 angle pdb=" C VAL A 408 " pdb=" CA VAL A 408 " pdb=" CB VAL A 408 " ideal model delta sigma weight residual 110.13 113.76 -3.63 9.70e-01 1.06e+00 1.40e+01 angle pdb=" C ASN A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N PRO A 93 " ideal model delta sigma weight residual 117.93 121.90 -3.97 1.20e+00 6.94e-01 1.09e+01 ... (remaining 14801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 6404 22.35 - 44.71: 218 44.71 - 67.06: 51 67.06 - 89.41: 26 89.41 - 111.76: 18 Dihedral angle restraints: 6717 sinusoidal: 2954 harmonic: 3763 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 -170.69 84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CA SER A 559 " pdb=" C SER A 559 " pdb=" N PRO A 560 " pdb=" CA PRO A 560 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 6714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1611 0.104 - 0.207: 147 0.207 - 0.311: 9 0.311 - 0.414: 4 0.414 - 0.518: 1 Chirality restraints: 1772 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 -1.88 -0.52 2.00e-01 2.50e+01 6.71e+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 3.47e+00 chirality pdb=" C17 CLR C 302 " pdb=" C13 CLR C 302 " pdb=" C16 CLR C 302 " pdb=" C20 CLR C 302 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1769 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO A 560 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 565 " -0.019 2.00e-02 2.50e+03 1.76e-02 6.19e+00 pdb=" CG TYR A 565 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 565 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 565 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 565 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 565 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 565 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 565 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.015 2.00e-02 2.50e+03 1.52e-02 5.76e+00 pdb=" CG TRP C 227 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2340 2.78 - 3.31: 9515 3.31 - 3.84: 17206 3.84 - 4.37: 19579 4.37 - 4.90: 34411 Nonbonded interactions: 83051 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.245 2.440 nonbonded pdb=" O SER A 234 " pdb=" OG SER A 238 " model vdw 2.295 2.440 nonbonded pdb=" O PHE B 86 " pdb=" OG1 THR B 90 " model vdw 2.299 2.440 nonbonded pdb=" CD2 LEU B 381 " pdb=" CE2 PHE B 386 " model vdw 2.311 3.760 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.316 2.440 ... (remaining 83046 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: 0.870 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: 2.400 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.090 Find NCS groups from input model: 0.310 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.010 0.081 10858 Z= 0.625 Angle : 1.060 11.991 14806 Z= 0.565 Chirality : 0.064 0.518 1772 Planarity : 0.007 0.065 1790 Dihedral : 14.519 111.763 4279 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.90 % Allowed : 1.90 % Favored : 97.20 % 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: -4.06 (0.18), residues: 1277 helix: -2.21 (0.15), residues: 674 sheet: -2.30 (0.43), residues: 128 loop : -3.36 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 227 HIS 0.021 0.003 HIS C 197 PHE 0.039 0.004 PHE C 132 TYR 0.042 0.003 TYR A 565 ARG 0.011 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8975 (mmt) cc_final: 0.8712 (mmm) REVERT: A 414 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8404 (ttm-80) REVERT: A 612 ASN cc_start: 0.8241 (m-40) cc_final: 0.7836 (t0) REVERT: A 649 THR cc_start: 0.9522 (p) cc_final: 0.9282 (p) REVERT: A 652 ARG cc_start: 0.8564 (mtp85) cc_final: 0.7968 (mtt180) REVERT: A 689 CYS cc_start: 0.8555 (t) cc_final: 0.8269 (t) REVERT: B 134 LEU cc_start: 0.8197 (mp) cc_final: 0.7963 (tp) REVERT: B 146 MET cc_start: 0.7454 (mmt) cc_final: 0.7218 (mmt) REVERT: B 244 TRP cc_start: 0.6966 (m-10) cc_final: 0.6355 (m100) REVERT: C 116 GLN cc_start: 0.8283 (mt0) cc_final: 0.7999 (mt0) REVERT: C 180 ASP cc_start: 0.8995 (t70) cc_final: 0.8554 (t0) REVERT: C 183 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7957 (mm-30) REVERT: D 34 ILE cc_start: 0.7041 (mt) cc_final: 0.6786 (mt) REVERT: D 52 GLN cc_start: 0.7668 (tt0) cc_final: 0.7213 (mm-40) REVERT: D 93 SER cc_start: 0.9623 (t) cc_final: 0.9317 (p) outliers start: 10 outliers final: 4 residues processed: 214 average time/residue: 0.2698 time to fit residues: 78.2199 Evaluate side-chains 112 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 149 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 313 GLN A 355 GLN A 392 ASN A 454 GLN A 531 ASN A 606 GLN A 610 HIS B 112 GLN B 222 GLN B 405 ASN D 8 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10858 Z= 0.173 Angle : 0.631 11.353 14806 Z= 0.311 Chirality : 0.043 0.271 1772 Planarity : 0.005 0.054 1790 Dihedral : 13.078 113.131 2029 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.99 % Allowed : 8.23 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1277 helix: -0.38 (0.19), residues: 679 sheet: -1.95 (0.42), residues: 131 loop : -2.87 (0.24), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 36 HIS 0.006 0.001 HIS C 197 PHE 0.023 0.002 PHE A 302 TYR 0.023 0.001 TYR B 446 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 612 ASN cc_start: 0.8267 (m-40) cc_final: 0.7933 (t0) REVERT: A 652 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8032 (mtt180) REVERT: A 683 SER cc_start: 0.9018 (t) cc_final: 0.8794 (p) REVERT: A 689 CYS cc_start: 0.8474 (t) cc_final: 0.8203 (t) REVERT: B 134 LEU cc_start: 0.8298 (mp) cc_final: 0.7883 (tt) REVERT: B 184 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 216 LYS cc_start: 0.7769 (tppt) cc_final: 0.7502 (tttt) REVERT: B 222 GLN cc_start: 0.8284 (tt0) cc_final: 0.8051 (tt0) REVERT: B 244 TRP cc_start: 0.6978 (m-10) cc_final: 0.6320 (m100) REVERT: C 60 THR cc_start: 0.8446 (t) cc_final: 0.8214 (t) REVERT: C 116 GLN cc_start: 0.8275 (mt0) cc_final: 0.7901 (mp10) REVERT: C 180 ASP cc_start: 0.8928 (t70) cc_final: 0.8501 (t0) REVERT: C 187 TYR cc_start: 0.8146 (m-80) cc_final: 0.7914 (m-80) REVERT: D 17 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6047 (tttt) REVERT: D 34 ILE cc_start: 0.7177 (mt) cc_final: 0.6925 (mt) REVERT: D 36 TRP cc_start: 0.7920 (t60) cc_final: 0.7304 (t60) REVERT: D 40 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6888 (mp0) REVERT: D 52 GLN cc_start: 0.7384 (tt0) cc_final: 0.7045 (mm-40) REVERT: D 93 SER cc_start: 0.9560 (t) cc_final: 0.9296 (p) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.2187 time to fit residues: 48.0510 Evaluate side-chains 119 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 62 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN C 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10858 Z= 0.288 Angle : 0.640 12.558 14806 Z= 0.310 Chirality : 0.044 0.286 1772 Planarity : 0.004 0.053 1790 Dihedral : 10.798 110.167 2029 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.71 % Allowed : 10.13 % Favored : 86.17 % 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: -1.32 (0.23), residues: 1277 helix: 0.39 (0.20), residues: 691 sheet: -1.73 (0.43), residues: 129 loop : -2.61 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 36 HIS 0.007 0.001 HIS C 197 PHE 0.026 0.002 PHE A 302 TYR 0.025 0.001 TYR B 446 ARG 0.006 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9211 (tpp) cc_final: 0.8990 (tpp) REVERT: A 612 ASN cc_start: 0.8366 (m-40) cc_final: 0.7974 (t0) REVERT: A 652 ARG cc_start: 0.8612 (mtp85) cc_final: 0.7933 (mtt180) REVERT: B 134 LEU cc_start: 0.8297 (mp) cc_final: 0.7887 (tt) REVERT: B 244 TRP cc_start: 0.7216 (m-10) cc_final: 0.6471 (m100) REVERT: B 450 ASP cc_start: 0.8465 (t0) cc_final: 0.8207 (t0) REVERT: C 60 THR cc_start: 0.8500 (t) cc_final: 0.8241 (t) REVERT: C 116 GLN cc_start: 0.8254 (mt0) cc_final: 0.7879 (mp10) REVERT: C 152 ASP cc_start: 0.8839 (m-30) cc_final: 0.8621 (m-30) REVERT: C 180 ASP cc_start: 0.8957 (t70) cc_final: 0.8582 (t0) REVERT: D 34 ILE cc_start: 0.7297 (mt) cc_final: 0.7082 (mt) REVERT: D 36 TRP cc_start: 0.7891 (t60) cc_final: 0.7346 (t60) REVERT: D 40 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7021 (mp0) REVERT: D 52 GLN cc_start: 0.7340 (tt0) cc_final: 0.6967 (mm-40) REVERT: D 93 SER cc_start: 0.9480 (t) cc_final: 0.9225 (p) outliers start: 41 outliers final: 24 residues processed: 139 average time/residue: 0.2026 time to fit residues: 42.4401 Evaluate side-chains 119 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10858 Z= 0.148 Angle : 0.550 11.263 14806 Z= 0.266 Chirality : 0.042 0.250 1772 Planarity : 0.004 0.049 1790 Dihedral : 9.822 104.089 2029 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.71 % Allowed : 11.66 % Favored : 85.62 % 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 (0.24), residues: 1277 helix: 0.90 (0.20), residues: 685 sheet: -1.59 (0.44), residues: 131 loop : -2.29 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 209 HIS 0.004 0.001 HIS C 197 PHE 0.022 0.001 PHE A 302 TYR 0.020 0.001 TYR B 446 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 124 SER cc_start: 0.8959 (m) cc_final: 0.8724 (p) REVERT: A 225 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8027 (mt) REVERT: A 612 ASN cc_start: 0.8356 (m-40) cc_final: 0.7966 (t0) REVERT: A 652 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8299 (mtt180) REVERT: B 134 LEU cc_start: 0.8357 (mp) cc_final: 0.7922 (tt) REVERT: B 222 GLN cc_start: 0.8268 (tt0) cc_final: 0.7987 (pt0) REVERT: B 244 TRP cc_start: 0.7215 (m-10) cc_final: 0.6456 (m100) REVERT: B 454 GLN cc_start: 0.8587 (tp40) cc_final: 0.8198 (tp-100) REVERT: C 48 LEU cc_start: 0.8532 (mt) cc_final: 0.8190 (tp) REVERT: C 60 THR cc_start: 0.8375 (t) cc_final: 0.8102 (t) REVERT: C 180 ASP cc_start: 0.8880 (t70) cc_final: 0.8521 (t0) REVERT: D 36 TRP cc_start: 0.7766 (t60) cc_final: 0.7271 (t60) REVERT: D 40 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6943 (mp0) REVERT: D 52 GLN cc_start: 0.7284 (tt0) cc_final: 0.6965 (mm-40) outliers start: 30 outliers final: 19 residues processed: 137 average time/residue: 0.1872 time to fit residues: 39.1032 Evaluate side-chains 125 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10858 Z= 0.469 Angle : 0.726 15.759 14806 Z= 0.352 Chirality : 0.047 0.289 1772 Planarity : 0.005 0.053 1790 Dihedral : 9.761 98.512 2029 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.34 % Allowed : 12.03 % Favored : 83.63 % 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: -0.81 (0.24), residues: 1277 helix: 0.81 (0.20), residues: 699 sheet: -1.55 (0.44), residues: 131 loop : -2.42 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 36 HIS 0.007 0.002 HIS C 58 PHE 0.026 0.002 PHE A 302 TYR 0.022 0.002 TYR B 189 ARG 0.005 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 95 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 ASP cc_start: 0.7816 (t0) cc_final: 0.7597 (t0) REVERT: A 612 ASN cc_start: 0.8321 (m-40) cc_final: 0.7926 (t0) REVERT: A 652 ARG cc_start: 0.8626 (mtp85) cc_final: 0.7972 (mtt180) REVERT: B 134 LEU cc_start: 0.8169 (mp) cc_final: 0.7821 (tt) REVERT: B 222 GLN cc_start: 0.8316 (tt0) cc_final: 0.7865 (pt0) REVERT: B 244 TRP cc_start: 0.7338 (m-10) cc_final: 0.6511 (m100) REVERT: B 454 GLN cc_start: 0.8628 (tp40) cc_final: 0.8249 (tp-100) REVERT: C 60 THR cc_start: 0.8469 (t) cc_final: 0.8186 (t) REVERT: C 116 GLN cc_start: 0.8384 (mt0) cc_final: 0.8073 (mt0) REVERT: C 180 ASP cc_start: 0.8920 (t70) cc_final: 0.8585 (t0) REVERT: C 192 LEU cc_start: 0.8975 (tp) cc_final: 0.8601 (tt) REVERT: D 52 GLN cc_start: 0.7484 (tt0) cc_final: 0.7112 (mm-40) outliers start: 48 outliers final: 37 residues processed: 134 average time/residue: 0.2024 time to fit residues: 40.4823 Evaluate side-chains 124 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10858 Z= 0.222 Angle : 0.590 13.331 14806 Z= 0.282 Chirality : 0.043 0.253 1772 Planarity : 0.004 0.045 1790 Dihedral : 9.218 90.595 2029 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.89 % Allowed : 13.83 % Favored : 83.27 % 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: -0.36 (0.24), residues: 1277 helix: 1.27 (0.21), residues: 682 sheet: -1.46 (0.44), residues: 131 loop : -2.20 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.004 0.001 HIS C 197 PHE 0.021 0.001 PHE A 302 TYR 0.019 0.001 TYR B 446 ARG 0.011 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 540 GLN cc_start: 0.8918 (tt0) cc_final: 0.8543 (tp40) REVERT: A 548 ASP cc_start: 0.7754 (t0) cc_final: 0.7418 (t0) REVERT: A 612 ASN cc_start: 0.8305 (m-40) cc_final: 0.7942 (t0) REVERT: A 652 ARG cc_start: 0.8582 (mtp85) cc_final: 0.7907 (mtt180) REVERT: B 134 LEU cc_start: 0.8165 (mp) cc_final: 0.7814 (tt) REVERT: B 222 GLN cc_start: 0.8326 (tt0) cc_final: 0.8039 (pt0) REVERT: B 244 TRP cc_start: 0.7318 (m-10) cc_final: 0.6489 (m100) REVERT: B 454 GLN cc_start: 0.8528 (tp40) cc_final: 0.8297 (tp-100) REVERT: C 48 LEU cc_start: 0.8640 (mt) cc_final: 0.8210 (tp) REVERT: C 60 THR cc_start: 0.8433 (t) cc_final: 0.8165 (t) REVERT: C 116 GLN cc_start: 0.8232 (mt0) cc_final: 0.7924 (mt0) REVERT: C 180 ASP cc_start: 0.8862 (t70) cc_final: 0.8540 (t0) REVERT: D 52 GLN cc_start: 0.7427 (tt0) cc_final: 0.7079 (mm-40) outliers start: 32 outliers final: 26 residues processed: 127 average time/residue: 0.1904 time to fit residues: 36.8579 Evaluate side-chains 121 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 56 optimal weight: 0.8980 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10858 Z= 0.289 Angle : 0.615 14.130 14806 Z= 0.294 Chirality : 0.044 0.258 1772 Planarity : 0.004 0.043 1790 Dihedral : 8.991 84.187 2029 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.71 % Allowed : 13.20 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.24), residues: 1277 helix: 1.32 (0.21), residues: 681 sheet: -1.46 (0.45), residues: 131 loop : -2.13 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS C 58 PHE 0.023 0.001 PHE A 302 TYR 0.018 0.001 TYR B 446 ARG 0.005 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 548 ASP cc_start: 0.7841 (t0) cc_final: 0.7617 (t0) REVERT: A 612 ASN cc_start: 0.8307 (m-40) cc_final: 0.7946 (t0) REVERT: A 652 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8002 (mtt180) REVERT: B 134 LEU cc_start: 0.8170 (mp) cc_final: 0.7818 (tt) REVERT: B 222 GLN cc_start: 0.8338 (tt0) cc_final: 0.8077 (pt0) REVERT: B 244 TRP cc_start: 0.7340 (m-10) cc_final: 0.6460 (m100) REVERT: C 48 LEU cc_start: 0.8642 (mt) cc_final: 0.8220 (tp) REVERT: C 60 THR cc_start: 0.8451 (t) cc_final: 0.8183 (t) REVERT: C 116 GLN cc_start: 0.8365 (mt0) cc_final: 0.8060 (mt0) REVERT: C 180 ASP cc_start: 0.8873 (t70) cc_final: 0.8556 (t0) REVERT: D 52 GLN cc_start: 0.7441 (tt0) cc_final: 0.7092 (mm-40) outliers start: 41 outliers final: 32 residues processed: 128 average time/residue: 0.1785 time to fit residues: 35.5620 Evaluate side-chains 124 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10858 Z= 0.157 Angle : 0.558 12.187 14806 Z= 0.265 Chirality : 0.042 0.237 1772 Planarity : 0.003 0.040 1790 Dihedral : 8.430 75.192 2029 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.98 % Allowed : 13.92 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.25), residues: 1277 helix: 1.46 (0.21), residues: 686 sheet: -1.47 (0.45), residues: 134 loop : -2.07 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.022 0.001 PHE A 302 TYR 0.016 0.001 TYR B 446 ARG 0.006 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 ASP cc_start: 0.7818 (t0) cc_final: 0.7586 (t0) REVERT: A 612 ASN cc_start: 0.8295 (m-40) cc_final: 0.7948 (t0) REVERT: A 652 ARG cc_start: 0.8630 (mtp85) cc_final: 0.7925 (mtt180) REVERT: B 134 LEU cc_start: 0.8213 (mp) cc_final: 0.7848 (tt) REVERT: B 222 GLN cc_start: 0.8279 (tt0) cc_final: 0.8035 (pt0) REVERT: B 244 TRP cc_start: 0.7272 (m-10) cc_final: 0.6381 (m100) REVERT: B 454 GLN cc_start: 0.8459 (tp40) cc_final: 0.8143 (tp-100) REVERT: C 48 LEU cc_start: 0.8588 (mt) cc_final: 0.8205 (tp) REVERT: C 60 THR cc_start: 0.8427 (t) cc_final: 0.8178 (t) REVERT: C 116 GLN cc_start: 0.8282 (mt0) cc_final: 0.7879 (mt0) REVERT: C 180 ASP cc_start: 0.8868 (t70) cc_final: 0.8583 (t0) REVERT: D 52 GLN cc_start: 0.7415 (tt0) cc_final: 0.7079 (mm-40) outliers start: 33 outliers final: 27 residues processed: 131 average time/residue: 0.1872 time to fit residues: 37.5373 Evaluate side-chains 125 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10858 Z= 0.307 Angle : 0.625 14.686 14806 Z= 0.298 Chirality : 0.044 0.234 1772 Planarity : 0.004 0.042 1790 Dihedral : 8.276 74.572 2027 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.16 % Allowed : 13.65 % Favored : 83.18 % 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: -0.16 (0.25), residues: 1277 helix: 1.41 (0.21), residues: 687 sheet: -1.44 (0.45), residues: 130 loop : -2.08 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.023 0.001 PHE A 302 TYR 0.018 0.001 TYR B 446 ARG 0.006 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8380 (mt) REVERT: A 548 ASP cc_start: 0.7937 (t0) cc_final: 0.7712 (t0) REVERT: A 612 ASN cc_start: 0.8316 (m-40) cc_final: 0.7976 (t0) REVERT: A 652 ARG cc_start: 0.8658 (mtp85) cc_final: 0.7989 (mtt180) REVERT: B 134 LEU cc_start: 0.8263 (mp) cc_final: 0.7869 (tt) REVERT: B 244 TRP cc_start: 0.7219 (m-10) cc_final: 0.6326 (m100) REVERT: C 48 LEU cc_start: 0.8624 (mt) cc_final: 0.8173 (tp) REVERT: C 60 THR cc_start: 0.8503 (t) cc_final: 0.8265 (t) REVERT: C 116 GLN cc_start: 0.8338 (mt0) cc_final: 0.7941 (mt0) REVERT: C 180 ASP cc_start: 0.8859 (t70) cc_final: 0.8593 (t0) REVERT: D 52 GLN cc_start: 0.7418 (tt0) cc_final: 0.7079 (mm-40) outliers start: 35 outliers final: 32 residues processed: 125 average time/residue: 0.1797 time to fit residues: 35.3037 Evaluate side-chains 126 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10858 Z= 0.247 Angle : 0.600 13.691 14806 Z= 0.284 Chirality : 0.043 0.233 1772 Planarity : 0.004 0.041 1790 Dihedral : 7.984 74.612 2027 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.98 % Allowed : 14.10 % Favored : 82.91 % 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: -0.07 (0.25), residues: 1277 helix: 1.47 (0.21), residues: 687 sheet: -1.43 (0.45), residues: 130 loop : -2.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.023 0.001 PHE A 302 TYR 0.017 0.001 TYR B 446 ARG 0.006 0.000 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (mt) REVERT: A 612 ASN cc_start: 0.8284 (m-40) cc_final: 0.7956 (t0) REVERT: A 652 ARG cc_start: 0.8648 (mtp85) cc_final: 0.7978 (mtt180) REVERT: B 134 LEU cc_start: 0.8260 (mp) cc_final: 0.7870 (tt) REVERT: B 244 TRP cc_start: 0.7218 (m-10) cc_final: 0.6300 (m100) REVERT: C 48 LEU cc_start: 0.8624 (mt) cc_final: 0.8168 (tp) REVERT: C 60 THR cc_start: 0.8467 (t) cc_final: 0.8198 (t) REVERT: C 116 GLN cc_start: 0.8317 (mt0) cc_final: 0.7931 (mt0) REVERT: C 180 ASP cc_start: 0.8839 (t70) cc_final: 0.8572 (t0) REVERT: D 52 GLN cc_start: 0.7405 (tt0) cc_final: 0.7073 (mm-40) outliers start: 33 outliers final: 30 residues processed: 126 average time/residue: 0.1914 time to fit residues: 36.8953 Evaluate side-chains 126 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.078880 restraints weight = 21809.938| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.91 r_work: 0.2860 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10858 Z= 0.161 Angle : 0.558 12.424 14806 Z= 0.265 Chirality : 0.041 0.237 1772 Planarity : 0.003 0.040 1790 Dihedral : 7.616 74.151 2027 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.98 % Allowed : 14.01 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1277 helix: 1.63 (0.21), residues: 683 sheet: -1.33 (0.46), residues: 129 loop : -1.95 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.022 0.001 PHE A 302 TYR 0.017 0.001 TYR B 446 ARG 0.007 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.68 seconds wall clock time: 38 minutes 23.50 seconds (2303.50 seconds total)