Starting phenix.real_space_refine on Thu Mar 21 09:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d42_27172/03_2024/8d42_27172_neut_trim_updated.pdb" } resolution = 2.91 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= -0.121 sd= 0.790 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 45 5.49 5 S 82 5.16 5 C 9546 2.51 5 N 2665 2.21 5 O 2852 1.98 5 H 14610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 15393 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6613 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6431 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 666 Classifications: {'DNA': 21} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 669 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.53, per 1000 atoms: 0.42 Number of scatterers: 29803 At special positions: 0 Unit cell: (115.6, 105.4, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 82 16.00 P 45 15.00 O 2852 8.00 N 2665 7.00 C 9546 6.00 H 14610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 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 Time building additional restraints: 22.16 Conformation dependent library (CDL) restraints added in 3.0 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 10 sheets defined 41.6% alpha, 12.6% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 15.61 Creating SS restraints... Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.633A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 135 through 158 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.749A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 417 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 439 through 481 removed outlier: 4.016A pdb=" N GLN A 472 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.536A pdb=" N GLY A 554 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.919A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 603 removed outlier: 4.011A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 788 through 809 removed outlier: 4.767A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 975 through 989 removed outlier: 3.985A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1065 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1085 through 1088 No H-bonds generated for 'chain 'A' and resid 1085 through 1088' Processing helix chain 'A' and resid 1093 through 1123 removed outlier: 3.686A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 4.931A pdb=" N TYR A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A1149 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1206 through 1209 No H-bonds generated for 'chain 'A' and resid 1206 through 1209' Processing helix chain 'A' and resid 1220 through 1227 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.182A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 removed outlier: 4.661A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 200 " --> pdb=" O CYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 468 through 484 removed outlier: 5.663A pdb=" N LYS B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.578A pdb=" N GLU C 155 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE C 156 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C 157 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 186 through 196 removed outlier: 3.634A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 248 through 265 Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.660A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 409 removed outlier: 4.484A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.323A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.721A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 265 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE A 197 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 267 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL A 199 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 290 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY A 268 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 292 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 435 through 438 Processing sheet with id= C, first strand: chain 'A' and resid 612 through 614 Processing sheet with id= D, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 3.509A pdb=" N ASP A1186 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.609A pdb=" N GLY B 207 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER B 337 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN B 305 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN B 339 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU B 303 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP B 341 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 301 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 326 Processing sheet with id= G, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.192A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE B 439 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.732A pdb=" N GLY C 207 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER C 337 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN C 305 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN C 339 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU C 303 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP C 341 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU C 301 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 289 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR C 302 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN C 287 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 323 through 326 Processing sheet with id= J, first strand: chain 'C' and resid 439 through 442 556 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.90 Time building geometry restraints manager: 23.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14576 1.03 - 1.23: 66 1.23 - 1.42: 6671 1.42 - 1.62: 8825 1.62 - 1.81: 131 Bond restraints: 30269 Sorted by residual: bond pdb=" O5' DCP A1304 " pdb=" PA DCP A1304 " ideal model delta sigma weight residual 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.27e+02 bond pdb=" C5' DCP A1304 " pdb=" O5' DCP A1304 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 1.592 1.710 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C4' DCP A1304 " pdb=" C5' DCP A1304 " ideal model delta sigma weight residual 1.508 1.563 -0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 1.600 1.651 -0.051 1.10e-02 8.26e+03 2.19e+01 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 92.82 - 101.18: 48 101.18 - 109.53: 20804 109.53 - 117.89: 19485 117.89 - 126.24: 13791 126.24 - 134.60: 600 Bond angle restraints: 54728 Sorted by residual: angle pdb=" O1G DCP A1304 " pdb=" PG DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 110.47 98.05 12.42 1.64e+00 3.70e-01 5.71e+01 angle pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 139.87 133.43 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" O2A DCP A1304 " pdb=" PA DCP A1304 " pdb=" O3A DCP A1304 " ideal model delta sigma weight residual 106.94 116.95 -10.01 1.88e+00 2.83e-01 2.84e+01 angle pdb=" C1' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" C6 DCP A1304 " ideal model delta sigma weight residual 121.66 114.29 7.37 1.39e+00 5.21e-01 2.82e+01 angle pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 101.57 93.51 8.06 1.54e+00 4.24e-01 2.76e+01 ... (remaining 54723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 13596 34.74 - 69.48: 459 69.48 - 104.22: 9 104.22 - 138.95: 0 138.95 - 173.69: 1 Dihedral angle restraints: 14065 sinusoidal: 7902 harmonic: 6163 Sorted by residual: dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DG T 5 " pdb=" C3' DG T 5 " pdb=" O3' DG T 5 " pdb=" P DT T 6 " ideal model delta sinusoidal sigma weight residual -140.00 33.69 -173.69 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1550 0.029 - 0.058: 497 0.058 - 0.087: 143 0.087 - 0.116: 96 0.116 - 0.145: 20 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C1' DCP A1304 " pdb=" C2' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" O4' DCP A1304 " both_signs ideal model delta sigma weight residual False 2.45 2.30 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL C 338 " pdb=" N VAL C 338 " pdb=" C VAL C 338 " pdb=" CB VAL C 338 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2303 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 485 " 0.029 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C VAL C 485 " -0.103 2.00e-02 2.50e+03 pdb=" O VAL C 485 " 0.037 2.00e-02 2.50e+03 pdb=" OXT VAL C 485 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 448 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ALA A 448 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA A 448 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 449 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 457 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 457 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 457 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 458 " 0.008 2.00e-02 2.50e+03 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1075 2.16 - 2.77: 56191 2.77 - 3.38: 81599 3.38 - 3.99: 104641 3.99 - 4.60: 164037 Nonbonded interactions: 407543 Sorted by model distance: nonbonded pdb=" OE1 GLU A1144 " pdb=" H GLU A1144 " model vdw 1.552 1.850 nonbonded pdb=" H VAL A 201 " pdb=" O3' DT P 24 " model vdw 1.564 1.850 nonbonded pdb=" HH TYR A 150 " pdb=" O ARG A 288 " model vdw 1.587 1.850 nonbonded pdb=" O THR B 447 " pdb=" H GLY B 451 " model vdw 1.597 1.850 nonbonded pdb=" OE1 GLU C 310 " pdb=" H GLU C 310 " model vdw 1.617 1.850 ... (remaining 407538 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 'B' and ((resid 67 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 68 through 218 or (resid 219 and (name N or \ name CA or name C or name O or name CB or name H or name HA or name HB2 or name \ HB3)) or (resid 228 and (name N or name CA or name C or name O or name CB or nam \ e HA or name HB )) or resid 229 through 355 or (resid 368 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 o \ r name NE2 or name HA or name HB2 or name HB3)) or resid 369 through 485)) selection = (chain 'C' and (resid 67 through 215 or (resid 216 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 217 through 355 or (resid 368 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name HA or name HB2 or name HB3)) or resid 369 through 485)) } 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: 2.310 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: 0.430 Extract box with map and model: 8.510 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 99.990 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 15659 Z= 0.178 Angle : 0.555 12.790 21406 Z= 0.310 Chirality : 0.037 0.145 2306 Planarity : 0.004 0.059 2600 Dihedral : 14.520 173.693 5921 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.84 % Allowed : 5.81 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1758 helix: 0.92 (0.21), residues: 713 sheet: 0.56 (0.31), residues: 258 loop : -0.20 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 620 HIS 0.003 0.001 HIS B 313 PHE 0.012 0.001 PHE C 403 TYR 0.008 0.001 TYR A 434 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 435 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8163 (t0) cc_final: 0.7825 (t0) REVERT: A 361 ARG cc_start: 0.7615 (tmt-80) cc_final: 0.7139 (tpm170) REVERT: A 610 PHE cc_start: 0.7513 (m-80) cc_final: 0.7261 (m-80) REVERT: A 743 ASP cc_start: 0.7133 (p0) cc_final: 0.6831 (p0) REVERT: A 793 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8038 (mp0) REVERT: A 797 MET cc_start: 0.8071 (mtt) cc_final: 0.7762 (mtp) REVERT: A 994 TRP cc_start: 0.4383 (m-90) cc_final: 0.3987 (m-10) REVERT: A 1138 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (mmt-90) REVERT: A 1192 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 249 ASN cc_start: 0.8076 (m-40) cc_final: 0.7773 (t0) REVERT: C 107 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7414 (mtm110) REVERT: C 129 ASP cc_start: 0.8193 (t70) cc_final: 0.7965 (t0) outliers start: 13 outliers final: 5 residues processed: 443 average time/residue: 2.1232 time to fit residues: 1061.4769 Evaluate side-chains 396 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 390 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 264 GLN A 843 GLN B 192 HIS B 250 GLN B 258 HIS B 292 ASN B 339 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15659 Z= 0.300 Angle : 0.578 4.758 21406 Z= 0.311 Chirality : 0.040 0.161 2306 Planarity : 0.005 0.063 2600 Dihedral : 14.572 172.794 2427 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.81 % Allowed : 14.02 % Favored : 82.17 % 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: 0.03 (0.20), residues: 1758 helix: 0.61 (0.20), residues: 715 sheet: 0.29 (0.32), residues: 251 loop : -0.52 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.005 0.001 HIS C 77 PHE 0.017 0.002 PHE A 539 TYR 0.019 0.002 TYR A 656 ARG 0.004 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 380 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: A 270 ASN cc_start: 0.8246 (t0) cc_final: 0.7801 (t0) REVERT: A 544 MET cc_start: 0.8053 (tmm) cc_final: 0.7758 (tmm) REVERT: A 779 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6107 (tt) REVERT: A 793 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8152 (mp0) REVERT: A 797 MET cc_start: 0.8087 (mtt) cc_final: 0.7793 (mtp) REVERT: A 1116 MET cc_start: 0.7598 (mmm) cc_final: 0.7370 (mmm) REVERT: A 1138 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7766 (mmt90) REVERT: A 1192 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 1233 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6157 (tptp) REVERT: C 107 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7493 (mtm110) REVERT: C 129 ASP cc_start: 0.8236 (t70) cc_final: 0.7973 (t0) REVERT: C 146 ARG cc_start: 0.6774 (mtp180) cc_final: 0.6309 (mtt90) REVERT: C 201 ASN cc_start: 0.8710 (t0) cc_final: 0.8460 (t0) REVERT: C 465 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.4672 (mpp) outliers start: 59 outliers final: 36 residues processed: 405 average time/residue: 2.1309 time to fit residues: 992.6607 Evaluate side-chains 407 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 366 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN B 339 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15659 Z= 0.389 Angle : 0.630 6.069 21406 Z= 0.342 Chirality : 0.042 0.167 2306 Planarity : 0.006 0.055 2600 Dihedral : 14.854 171.142 2425 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.46 % Allowed : 15.25 % Favored : 80.30 % 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: -0.65 (0.20), residues: 1758 helix: 0.02 (0.19), residues: 712 sheet: 0.22 (0.32), residues: 248 loop : -0.97 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 262 HIS 0.007 0.002 HIS B 313 PHE 0.019 0.002 PHE A1092 TYR 0.019 0.002 TYR C 206 ARG 0.007 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 378 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8521 (mmm) cc_final: 0.8300 (mmm) REVERT: A 94 MET cc_start: 0.6927 (pp-130) cc_final: 0.6628 (ppp) REVERT: A 270 ASN cc_start: 0.8313 (t0) cc_final: 0.8014 (t0) REVERT: A 430 MET cc_start: 0.8238 (tpt) cc_final: 0.7890 (tpt) REVERT: A 544 MET cc_start: 0.8057 (tmm) cc_final: 0.7814 (tmm) REVERT: A 610 PHE cc_start: 0.7676 (m-80) cc_final: 0.7364 (m-80) REVERT: A 659 HIS cc_start: 0.2391 (OUTLIER) cc_final: 0.2005 (m90) REVERT: A 743 ASP cc_start: 0.7115 (p0) cc_final: 0.6844 (p0) REVERT: A 793 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8213 (mp0) REVERT: A 797 MET cc_start: 0.8127 (mtt) cc_final: 0.7835 (mtp) REVERT: A 1138 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7556 (mmt90) REVERT: A 1192 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 1233 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6181 (tptp) REVERT: B 122 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8524 (mtt-85) REVERT: C 107 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7706 (mmm-85) REVERT: C 129 ASP cc_start: 0.8289 (t70) cc_final: 0.7958 (t70) REVERT: C 201 ASN cc_start: 0.8775 (t0) cc_final: 0.8502 (t0) REVERT: C 400 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: C 465 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.4648 (mpp) outliers start: 69 outliers final: 48 residues processed: 407 average time/residue: 2.0485 time to fit residues: 945.4467 Evaluate side-chains 412 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 258 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15659 Z= 0.396 Angle : 0.650 4.780 21406 Z= 0.353 Chirality : 0.042 0.158 2306 Planarity : 0.006 0.057 2600 Dihedral : 14.967 170.032 2425 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.30 % Allowed : 16.80 % Favored : 77.91 % 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: -1.02 (0.20), residues: 1758 helix: -0.23 (0.19), residues: 707 sheet: 0.26 (0.33), residues: 236 loop : -1.31 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 262 HIS 0.008 0.002 HIS C 96 PHE 0.018 0.002 PHE A 389 TYR 0.020 0.002 TYR C 206 ARG 0.007 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 369 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6941 (pp-130) cc_final: 0.6656 (ppp) REVERT: A 191 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: A 270 ASN cc_start: 0.8350 (t0) cc_final: 0.8013 (t0) REVERT: A 430 MET cc_start: 0.8255 (tpt) cc_final: 0.7946 (tpt) REVERT: A 610 PHE cc_start: 0.7532 (m-80) cc_final: 0.7210 (m-80) REVERT: A 743 ASP cc_start: 0.7132 (p0) cc_final: 0.6882 (p0) REVERT: A 793 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8197 (mp0) REVERT: A 797 MET cc_start: 0.8108 (mtt) cc_final: 0.7814 (mtp) REVERT: A 992 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7394 (pp) REVERT: A 1192 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 139 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5292 (pt) REVERT: C 107 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7598 (mtp180) REVERT: C 129 ASP cc_start: 0.8317 (t70) cc_final: 0.7919 (t0) REVERT: C 201 ASN cc_start: 0.8795 (t0) cc_final: 0.8496 (t0) REVERT: C 400 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: C 404 ASN cc_start: 0.7876 (m110) cc_final: 0.7426 (m110) outliers start: 82 outliers final: 54 residues processed: 410 average time/residue: 2.0311 time to fit residues: 951.6820 Evaluate side-chains 418 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 360 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 0.0030 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 258 HIS B 292 ASN B 330 ASN C 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15659 Z= 0.289 Angle : 0.599 5.710 21406 Z= 0.324 Chirality : 0.040 0.149 2306 Planarity : 0.005 0.059 2600 Dihedral : 14.898 171.157 2425 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.78 % Allowed : 17.51 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1758 helix: -0.01 (0.19), residues: 705 sheet: 0.29 (0.32), residues: 238 loop : -1.27 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 897 HIS 0.006 0.001 HIS B 313 PHE 0.016 0.002 PHE A1092 TYR 0.016 0.002 TYR C 206 ARG 0.004 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 369 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6947 (pp-130) cc_final: 0.6680 (ppp) REVERT: A 270 ASN cc_start: 0.8332 (t0) cc_final: 0.7962 (t0) REVERT: A 430 MET cc_start: 0.8263 (tpt) cc_final: 0.7943 (tpt) REVERT: A 743 ASP cc_start: 0.7123 (p0) cc_final: 0.6861 (p0) REVERT: A 793 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8159 (mp0) REVERT: A 797 MET cc_start: 0.8098 (mtt) cc_final: 0.7796 (mtp) REVERT: A 992 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 1192 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 139 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5323 (pt) REVERT: C 107 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7601 (mtp180) REVERT: C 129 ASP cc_start: 0.8282 (t70) cc_final: 0.7932 (t0) REVERT: C 183 GLU cc_start: 0.7274 (tp30) cc_final: 0.7067 (tp30) REVERT: C 201 ASN cc_start: 0.8777 (t0) cc_final: 0.8494 (t0) REVERT: C 344 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7362 (mmt-90) REVERT: C 400 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: C 404 ASN cc_start: 0.7815 (m110) cc_final: 0.7345 (m110) REVERT: C 465 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.4679 (mpp) outliers start: 74 outliers final: 51 residues processed: 405 average time/residue: 2.0413 time to fit residues: 937.7851 Evaluate side-chains 414 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 358 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 175 optimal weight: 0.4980 chunk 145 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 overall best weight: 2.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 258 HIS B 292 ASN B 305 ASN C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 15659 Z= 0.240 Angle : 0.581 11.179 21406 Z= 0.311 Chirality : 0.039 0.201 2306 Planarity : 0.005 0.052 2600 Dihedral : 14.786 172.258 2425 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.72 % Allowed : 18.73 % Favored : 76.55 % 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: -0.60 (0.20), residues: 1758 helix: 0.18 (0.20), residues: 711 sheet: 0.36 (0.32), residues: 238 loop : -1.11 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 897 HIS 0.006 0.001 HIS B 313 PHE 0.016 0.001 PHE A1092 TYR 0.013 0.001 TYR C 206 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 375 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6939 (pp-130) cc_final: 0.6685 (ppp) REVERT: A 270 ASN cc_start: 0.8315 (t0) cc_final: 0.7934 (t0) REVERT: A 430 MET cc_start: 0.8247 (tpt) cc_final: 0.7938 (tpt) REVERT: A 610 PHE cc_start: 0.7616 (m-80) cc_final: 0.7238 (m-80) REVERT: A 743 ASP cc_start: 0.7113 (p0) cc_final: 0.6830 (p0) REVERT: A 793 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8166 (mp0) REVERT: A 797 MET cc_start: 0.8095 (mtt) cc_final: 0.7786 (mtp) REVERT: A 992 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7361 (pp) REVERT: A 1138 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7574 (mmt90) REVERT: B 139 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5326 (pt) REVERT: B 418 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9013 (mt) REVERT: C 107 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7593 (mtp180) REVERT: C 129 ASP cc_start: 0.8264 (t70) cc_final: 0.7977 (t0) REVERT: C 201 ASN cc_start: 0.8749 (t0) cc_final: 0.8498 (t0) REVERT: C 344 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7389 (mmt-90) REVERT: C 400 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: C 404 ASN cc_start: 0.7789 (m110) cc_final: 0.7317 (m110) outliers start: 73 outliers final: 47 residues processed: 413 average time/residue: 2.0455 time to fit residues: 965.9863 Evaluate side-chains 420 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 367 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN B 330 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15659 Z= 0.223 Angle : 0.578 15.874 21406 Z= 0.307 Chirality : 0.039 0.187 2306 Planarity : 0.005 0.049 2600 Dihedral : 14.736 173.009 2425 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.13 % Allowed : 19.77 % Favored : 76.10 % 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: -0.47 (0.20), residues: 1758 helix: 0.31 (0.20), residues: 709 sheet: 0.40 (0.32), residues: 231 loop : -1.04 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 897 HIS 0.005 0.001 HIS C 96 PHE 0.016 0.001 PHE A 197 TYR 0.013 0.001 TYR C 206 ARG 0.003 0.000 ARG A1208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 370 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6929 (pp-130) cc_final: 0.6653 (ppp) REVERT: A 270 ASN cc_start: 0.8304 (t0) cc_final: 0.7921 (t0) REVERT: A 430 MET cc_start: 0.8228 (tpt) cc_final: 0.7902 (tpt) REVERT: A 610 PHE cc_start: 0.7541 (m-80) cc_final: 0.7225 (m-80) REVERT: A 743 ASP cc_start: 0.7112 (p0) cc_final: 0.6833 (p0) REVERT: A 793 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8159 (mp0) REVERT: A 797 MET cc_start: 0.8092 (mtt) cc_final: 0.7789 (mtp) REVERT: A 992 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7383 (pp) REVERT: A 1138 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7593 (mmt90) REVERT: B 418 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9001 (mt) REVERT: C 107 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7595 (mtp180) REVERT: C 129 ASP cc_start: 0.8248 (t70) cc_final: 0.7966 (t0) REVERT: C 201 ASN cc_start: 0.8732 (t0) cc_final: 0.8485 (t0) REVERT: C 344 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7290 (mmt-90) REVERT: C 400 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: C 404 ASN cc_start: 0.7757 (m110) cc_final: 0.7277 (m110) REVERT: C 465 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.4704 (mpp) outliers start: 64 outliers final: 44 residues processed: 405 average time/residue: 2.0606 time to fit residues: 946.1126 Evaluate side-chains 416 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 366 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN B 305 ASN C 261 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15659 Z= 0.420 Angle : 0.675 14.960 21406 Z= 0.364 Chirality : 0.043 0.172 2306 Planarity : 0.006 0.051 2600 Dihedral : 15.111 171.878 2425 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.78 % Allowed : 19.25 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1758 helix: -0.15 (0.19), residues: 699 sheet: 0.31 (0.33), residues: 231 loop : -1.45 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 262 HIS 0.008 0.002 HIS B 313 PHE 0.019 0.002 PHE A 197 TYR 0.018 0.002 TYR C 206 ARG 0.007 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 369 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6924 (pp-130) cc_final: 0.6670 (ppp) REVERT: A 270 ASN cc_start: 0.8328 (t0) cc_final: 0.8072 (t0) REVERT: A 430 MET cc_start: 0.8289 (tpt) cc_final: 0.7951 (tpt) REVERT: A 610 PHE cc_start: 0.7465 (m-80) cc_final: 0.7122 (m-80) REVERT: A 743 ASP cc_start: 0.7138 (p0) cc_final: 0.6877 (p0) REVERT: A 793 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8193 (mp0) REVERT: A 797 MET cc_start: 0.8117 (mtt) cc_final: 0.7810 (mtp) REVERT: A 1138 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7785 (mmt90) REVERT: B 139 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5301 (pt) REVERT: C 107 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7637 (mtp180) REVERT: C 129 ASP cc_start: 0.8281 (t70) cc_final: 0.7936 (t0) REVERT: C 201 ASN cc_start: 0.8749 (t0) cc_final: 0.8462 (t0) REVERT: C 344 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7375 (mmt-90) REVERT: C 400 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: C 404 ASN cc_start: 0.7846 (m110) cc_final: 0.7396 (m110) outliers start: 74 outliers final: 56 residues processed: 412 average time/residue: 2.0792 time to fit residues: 975.4215 Evaluate side-chains 429 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 369 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 chunk 97 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 153 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15659 Z= 0.180 Angle : 0.574 12.476 21406 Z= 0.304 Chirality : 0.039 0.165 2306 Planarity : 0.005 0.053 2600 Dihedral : 14.752 173.017 2425 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.65 % Allowed : 21.45 % Favored : 75.90 % 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: -0.47 (0.20), residues: 1758 helix: 0.33 (0.20), residues: 704 sheet: 0.40 (0.32), residues: 237 loop : -1.05 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 897 HIS 0.005 0.001 HIS C 258 PHE 0.017 0.001 PHE A 197 TYR 0.012 0.001 TYR C 206 ARG 0.004 0.000 ARG A1208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 419 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 378 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6885 (pp-130) cc_final: 0.6603 (ppp) REVERT: A 270 ASN cc_start: 0.8286 (t0) cc_final: 0.7939 (t0) REVERT: A 430 MET cc_start: 0.8244 (tpt) cc_final: 0.7912 (tpt) REVERT: A 743 ASP cc_start: 0.7052 (p0) cc_final: 0.6827 (p0) REVERT: A 793 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8126 (mp0) REVERT: A 797 MET cc_start: 0.8083 (mtt) cc_final: 0.7775 (mtp) REVERT: A 1138 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7636 (mmt90) REVERT: B 139 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5318 (pt) REVERT: B 418 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8998 (mt) REVERT: C 107 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7646 (mtp180) REVERT: C 129 ASP cc_start: 0.8215 (t70) cc_final: 0.7943 (t0) REVERT: C 201 ASN cc_start: 0.8723 (t0) cc_final: 0.8494 (t0) REVERT: C 314 MET cc_start: 0.7824 (ttm) cc_final: 0.7528 (ttm) REVERT: C 400 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: C 404 ASN cc_start: 0.7717 (m110) cc_final: 0.7236 (m110) REVERT: C 465 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.4750 (mpp) outliers start: 41 outliers final: 30 residues processed: 400 average time/residue: 2.0489 time to fit residues: 931.0532 Evaluate side-chains 405 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 370 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 143 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN B 305 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15659 Z= 0.273 Angle : 0.603 12.423 21406 Z= 0.321 Chirality : 0.040 0.169 2306 Planarity : 0.005 0.052 2600 Dihedral : 14.855 172.967 2425 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.58 % Allowed : 21.77 % Favored : 75.65 % 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: -0.61 (0.20), residues: 1758 helix: 0.28 (0.20), residues: 698 sheet: 0.37 (0.32), residues: 237 loop : -1.21 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 620 HIS 0.006 0.001 HIS C 258 PHE 0.016 0.002 PHE A 197 TYR 0.017 0.002 TYR B 291 ARG 0.004 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 371 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.6877 (pp-130) cc_final: 0.6593 (ppp) REVERT: A 270 ASN cc_start: 0.8354 (t0) cc_final: 0.7998 (t0) REVERT: A 430 MET cc_start: 0.8260 (tpt) cc_final: 0.7923 (tpt) REVERT: A 743 ASP cc_start: 0.7104 (p0) cc_final: 0.6878 (p0) REVERT: A 793 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8148 (mp0) REVERT: A 797 MET cc_start: 0.8102 (mtt) cc_final: 0.7798 (mtp) REVERT: A 1138 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7596 (mmt90) REVERT: B 139 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5324 (pt) REVERT: B 418 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9009 (mt) REVERT: C 107 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7654 (mtp180) REVERT: C 129 ASP cc_start: 0.8255 (t70) cc_final: 0.8015 (t0) REVERT: C 201 ASN cc_start: 0.8750 (t0) cc_final: 0.8513 (t0) REVERT: C 314 MET cc_start: 0.7868 (ttm) cc_final: 0.7577 (ttm) REVERT: C 400 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: C 404 ASN cc_start: 0.7773 (m110) cc_final: 0.7324 (m110) REVERT: C 465 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.4776 (mpp) outliers start: 40 outliers final: 34 residues processed: 392 average time/residue: 2.0478 time to fit residues: 912.2559 Evaluate side-chains 407 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 368 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 843 GLN B 192 HIS B 292 ASN B 330 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121280 restraints weight = 81428.290| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.12 r_work: 0.3570 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15659 Z= 0.167 Angle : 0.560 11.223 21406 Z= 0.295 Chirality : 0.038 0.173 2306 Planarity : 0.005 0.048 2600 Dihedral : 14.589 173.642 2425 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.07 % Allowed : 22.29 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1758 helix: 0.64 (0.20), residues: 702 sheet: 0.22 (0.32), residues: 244 loop : -0.90 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 897 HIS 0.005 0.001 HIS C 258 PHE 0.016 0.001 PHE A 197 TYR 0.012 0.001 TYR A1108 ARG 0.004 0.000 ARG A 852 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13885.99 seconds wall clock time: 241 minutes 36.96 seconds (14496.96 seconds total)