Starting phenix.real_space_refine on Sun Dec 10 05:59:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1i_29671/12_2023/8g1i_29671.pdb" } resolution = 3.12 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 22 5.16 5 C 8141 2.51 5 N 2385 2.21 5 O 2924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A GLU 1260": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13613 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2091 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "A" Number of atoms: 10616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 10616 Classifications: {'peptide': 1298} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 34, 'TRANS': 1263} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Time building chain proxies: 8.09, per 1000 atoms: 0.59 Number of scatterers: 13613 At special positions: 0 Unit cell: (95.9, 119, 133.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 141 15.00 O 2924 8.00 N 2385 7.00 C 8141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 6.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 48.8% alpha, 6.2% beta 24 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.017A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.801A pdb=" N LEU A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.785A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.149A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.506A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.564A pdb=" N THR A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.281A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.748A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.922A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.184A pdb=" N LEU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.820A pdb=" N TYR A 325 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.064A pdb=" N THR A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.696A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.636A pdb=" N LEU A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.350A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 416 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.904A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 436' Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.700A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.524A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 removed outlier: 3.533A pdb=" N TYR A 521 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.615A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.571A pdb=" N HIS A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.931A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 628 through 638 removed outlier: 4.209A pdb=" N THR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 removed outlier: 4.286A pdb=" N LYS A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.719A pdb=" N LEU A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 712 removed outlier: 4.565A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 735 through 751 removed outlier: 4.010A pdb=" N GLN A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.549A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 872 through 886 removed outlier: 5.439A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.545A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 980 through 983 Processing helix chain 'A' and resid 984 through 1001 removed outlier: 4.137A pdb=" N TYR A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 989 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1000 " --> pdb=" O ALA A 996 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 removed outlier: 4.438A pdb=" N SER A1006 " --> pdb=" O LYS A1003 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A1007 " --> pdb=" O LEU A1004 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1003 through 1007' Processing helix chain 'A' and resid 1031 through 1042 Processing helix chain 'A' and resid 1043 through 1045 No H-bonds generated for 'chain 'A' and resid 1043 through 1045' Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.565A pdb=" N PHE A1174 " --> pdb=" O GLU A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.695A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1195' Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.833A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1262 removed outlier: 3.524A pdb=" N PHE A1258 " --> pdb=" O GLN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 Processing helix chain 'A' and resid 1267 through 1278 removed outlier: 3.946A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.616A pdb=" N LYS A1296 " --> pdb=" O SER A1292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1311 through 1315 removed outlier: 3.857A pdb=" N THR A1314 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1315 " --> pdb=" O LEU A1312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1311 through 1315' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.706A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.545A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 18 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 49 " --> pdb=" O TRP A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.509A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A1346 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1348 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A1212 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A1221 " --> pdb=" O MET A1213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 943 through 944 removed outlier: 3.596A pdb=" N LYS A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.509A pdb=" N GLU A1064 " --> pdb=" O TRP A1074 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.854A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3386 1.33 - 1.45: 3238 1.45 - 1.57: 7210 1.57 - 1.69: 279 1.69 - 1.81: 42 Bond restraints: 14155 Sorted by residual: bond pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.17e-02 7.31e+03 1.61e+01 bond pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" N TYR A 529 " pdb=" CA TYR A 529 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.32e+00 bond pdb=" N LYS A 526 " pdb=" CA LYS A 526 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.20e-02 6.94e+03 9.08e+00 bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.39e+00 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.14: 972 106.14 - 113.11: 7676 113.11 - 120.07: 5231 120.07 - 127.04: 5419 127.04 - 134.01: 413 Bond angle restraints: 19711 Sorted by residual: angle pdb=" N LEU A 289 " pdb=" CA LEU A 289 " pdb=" C LEU A 289 " ideal model delta sigma weight residual 113.19 105.00 8.19 1.19e+00 7.06e-01 4.73e+01 angle pdb=" C TYR A 529 " pdb=" N VAL A 530 " pdb=" CA VAL A 530 " ideal model delta sigma weight residual 123.14 117.36 5.78 1.31e+00 5.83e-01 1.95e+01 angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 113.30 107.41 5.89 1.34e+00 5.57e-01 1.93e+01 angle pdb=" N PHE A 185 " pdb=" CA PHE A 185 " pdb=" C PHE A 185 " ideal model delta sigma weight residual 111.75 106.33 5.42 1.28e+00 6.10e-01 1.79e+01 angle pdb=" N ILE A 201 " pdb=" CA ILE A 201 " pdb=" C ILE A 201 " ideal model delta sigma weight residual 109.51 103.73 5.78 1.43e+00 4.89e-01 1.63e+01 ... (remaining 19706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 7791 33.86 - 67.72: 639 67.72 - 101.58: 54 101.58 - 135.44: 2 135.44 - 169.31: 2 Dihedral angle restraints: 8488 sinusoidal: 4673 harmonic: 3815 Sorted by residual: dihedral pdb=" CD ARG A 832 " pdb=" NE ARG A 832 " pdb=" CZ ARG A 832 " pdb=" NH1 ARG A 832 " ideal model delta sinusoidal sigma weight residual 0.00 68.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" C4' DT C 29 " pdb=" C3' DT C 29 " pdb=" O3' DT C 29 " pdb=" P DA C 30 " ideal model delta sinusoidal sigma weight residual 220.00 50.69 169.31 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA GLY A 906 " pdb=" C GLY A 906 " pdb=" N GLY A 907 " pdb=" CA GLY A 907 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 8485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2211 0.113 - 0.225: 50 0.225 - 0.338: 3 0.338 - 0.450: 0 0.450 - 0.563: 2 Chirality restraints: 2266 Sorted by residual: chirality pdb=" P DA D 39 " pdb=" OP1 DA D 39 " pdb=" OP2 DA D 39 " pdb=" O5' DA D 39 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" P DG D 40 " pdb=" OP1 DG D 40 " pdb=" OP2 DG D 40 " pdb=" O5' DG D 40 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ILE A 201 " pdb=" N ILE A 201 " pdb=" C ILE A 201 " pdb=" CB ILE A 201 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2263 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 832 " -1.019 9.50e-02 1.11e+02 4.57e-01 1.26e+02 pdb=" NE ARG A 832 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 832 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 832 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 832 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 377 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 378 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 525 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C THR A 525 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 525 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS A 526 " 0.018 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 64 2.56 - 3.15: 9658 3.15 - 3.73: 19525 3.73 - 4.31: 27188 4.31 - 4.90: 43679 Nonbonded interactions: 100114 Sorted by model distance: nonbonded pdb=" OE1 GLU A1007 " pdb=" OH TYR A1039 " model vdw 1.975 2.440 nonbonded pdb=" OP1 C B 4 " pdb=" OH TYR A 515 " model vdw 2.085 2.440 nonbonded pdb=" OG SER A1006 " pdb=" OE2 GLU A1007 " model vdw 2.173 2.440 nonbonded pdb=" ND2 ASN A1177 " pdb=" OD2 ASP A1180 " model vdw 2.186 2.520 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.216 2.440 ... (remaining 100109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.950 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.290 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.003 0.067 14155 Z= 0.213 Angle : 0.638 9.522 19711 Z= 0.372 Chirality : 0.045 0.563 2266 Planarity : 0.011 0.457 1996 Dihedral : 21.140 169.305 6014 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.72 % Allowed : 26.37 % Favored : 71.91 % 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: -1.85 (0.23), residues: 1280 helix: -0.38 (0.23), residues: 555 sheet: -0.94 (0.51), residues: 90 loop : -2.08 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 659 HIS 0.006 0.001 HIS A 41 PHE 0.019 0.001 PHE A 606 TYR 0.017 0.001 TYR A 192 ARG 0.009 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 219 average time/residue: 0.3735 time to fit residues: 109.2967 Evaluate side-chains 211 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1833 time to fit residues: 5.1663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.0570 chunk 128 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 GLN A 831 ASN A 863 ASN A 940 ASN A1256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14155 Z= 0.187 Angle : 0.542 6.893 19711 Z= 0.295 Chirality : 0.039 0.169 2266 Planarity : 0.004 0.063 1996 Dihedral : 19.432 163.936 3260 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.75 % Allowed : 25.00 % Favored : 72.25 % 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: -1.52 (0.23), residues: 1280 helix: -0.09 (0.23), residues: 554 sheet: -0.63 (0.51), residues: 101 loop : -1.94 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.007 0.001 HIS A1349 PHE 0.017 0.002 PHE A1134 TYR 0.013 0.001 TYR A 639 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.368 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 239 average time/residue: 0.3477 time to fit residues: 112.2136 Evaluate side-chains 217 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2659 time to fit residues: 5.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 0.0570 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 808 ASN A 940 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14155 Z= 0.301 Angle : 0.625 7.509 19711 Z= 0.339 Chirality : 0.042 0.170 2266 Planarity : 0.004 0.048 1996 Dihedral : 19.455 160.783 3260 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.32 % Allowed : 24.83 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1280 helix: -0.01 (0.22), residues: 562 sheet: -0.40 (0.50), residues: 109 loop : -2.11 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.009 0.002 HIS A1349 PHE 0.025 0.002 PHE A1134 TYR 0.019 0.002 TYR A 5 ARG 0.005 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.405 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 232 average time/residue: 0.3322 time to fit residues: 104.8362 Evaluate side-chains 220 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1651 time to fit residues: 5.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A1044 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14155 Z= 0.303 Angle : 0.606 6.365 19711 Z= 0.329 Chirality : 0.042 0.182 2266 Planarity : 0.004 0.052 1996 Dihedral : 19.403 158.666 3260 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.23 % Allowed : 25.95 % Favored : 71.82 % 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: -1.50 (0.23), residues: 1280 helix: 0.02 (0.22), residues: 563 sheet: -0.16 (0.50), residues: 106 loop : -2.17 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.010 0.001 HIS A1349 PHE 0.023 0.002 PHE A1134 TYR 0.021 0.002 TYR A 347 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 1.257 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 223 average time/residue: 0.3361 time to fit residues: 101.7634 Evaluate side-chains 206 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1262 time to fit residues: 4.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN A 194 GLN A 817 GLN A1044 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14155 Z= 0.273 Angle : 0.588 8.586 19711 Z= 0.320 Chirality : 0.041 0.182 2266 Planarity : 0.004 0.048 1996 Dihedral : 19.294 159.664 3260 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.80 % Allowed : 25.95 % Favored : 72.25 % 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: -1.39 (0.23), residues: 1280 helix: 0.16 (0.22), residues: 562 sheet: -0.20 (0.48), residues: 118 loop : -2.19 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.009 0.001 HIS A1349 PHE 0.021 0.002 PHE A1134 TYR 0.021 0.002 TYR A 347 ARG 0.006 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 219 average time/residue: 0.3434 time to fit residues: 102.3571 Evaluate side-chains 215 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1708 time to fit residues: 5.4840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 137 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14155 Z= 0.191 Angle : 0.519 5.814 19711 Z= 0.285 Chirality : 0.039 0.184 2266 Planarity : 0.004 0.044 1996 Dihedral : 19.103 162.081 3260 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 25.77 % Favored : 72.16 % 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: -1.17 (0.23), residues: 1280 helix: 0.37 (0.23), residues: 568 sheet: 0.02 (0.49), residues: 114 loop : -2.14 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.011 0.001 HIS A 328 PHE 0.022 0.001 PHE A 606 TYR 0.014 0.001 TYR A 347 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 212 average time/residue: 0.3547 time to fit residues: 101.7348 Evaluate side-chains 212 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1587 time to fit residues: 5.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 136 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1044 ASN A1295 ASN A1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14155 Z= 0.159 Angle : 0.491 6.915 19711 Z= 0.269 Chirality : 0.037 0.139 2266 Planarity : 0.003 0.041 1996 Dihedral : 19.022 165.576 3260 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.95 % Allowed : 26.72 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1280 helix: 0.61 (0.23), residues: 558 sheet: 0.21 (0.50), residues: 113 loop : -2.03 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 PHE 0.014 0.001 PHE A 606 TYR 0.013 0.001 TYR A 347 ARG 0.004 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 214 average time/residue: 0.3588 time to fit residues: 103.2846 Evaluate side-chains 209 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1305 time to fit residues: 2.9581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.0870 chunk 12 optimal weight: 0.0370 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1044 ASN A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14155 Z= 0.150 Angle : 0.481 6.846 19711 Z= 0.264 Chirality : 0.037 0.138 2266 Planarity : 0.003 0.040 1996 Dihedral : 18.942 167.005 3260 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.69 % Allowed : 27.32 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1280 helix: 0.61 (0.23), residues: 568 sheet: 0.31 (0.50), residues: 113 loop : -1.96 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 PHE 0.013 0.001 PHE A 606 TYR 0.013 0.001 TYR A 347 ARG 0.004 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.596 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 208 average time/residue: 0.3652 time to fit residues: 101.5202 Evaluate side-chains 208 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1916 time to fit residues: 3.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 0.0370 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 115 optimal weight: 0.0000 chunk 120 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14155 Z= 0.121 Angle : 0.453 7.297 19711 Z= 0.247 Chirality : 0.035 0.139 2266 Planarity : 0.003 0.040 1996 Dihedral : 18.849 167.068 3260 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.34 % Allowed : 28.01 % Favored : 71.65 % 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: -0.57 (0.24), residues: 1280 helix: 0.81 (0.23), residues: 570 sheet: 0.43 (0.49), residues: 115 loop : -1.79 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 606 TYR 0.008 0.001 TYR A 347 ARG 0.003 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 1.255 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 205 average time/residue: 0.3473 time to fit residues: 95.6044 Evaluate side-chains 193 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1580 time to fit residues: 2.0305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 50.0000 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 120 optimal weight: 0.0770 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14155 Z= 0.128 Angle : 0.464 6.226 19711 Z= 0.252 Chirality : 0.036 0.180 2266 Planarity : 0.003 0.041 1996 Dihedral : 18.834 168.004 3260 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.17 % Allowed : 28.52 % Favored : 71.31 % 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: -0.48 (0.24), residues: 1280 helix: 0.90 (0.23), residues: 570 sheet: 0.46 (0.49), residues: 117 loop : -1.76 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.012 0.001 PHE A 606 TYR 0.009 0.001 TYR A 347 ARG 0.004 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.353 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 202 average time/residue: 0.3549 time to fit residues: 96.5839 Evaluate side-chains 198 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1612 time to fit residues: 2.1552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138079 restraints weight = 18716.426| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.26 r_work: 0.3193 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14155 Z= 0.146 Angle : 0.479 5.966 19711 Z= 0.261 Chirality : 0.036 0.155 2266 Planarity : 0.003 0.041 1996 Dihedral : 18.800 168.160 3260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.52 % Allowed : 27.92 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1280 helix: 0.96 (0.23), residues: 564 sheet: 0.49 (0.50), residues: 113 loop : -1.80 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 PHE 0.012 0.001 PHE A 606 TYR 0.013 0.001 TYR A 347 ARG 0.003 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.08 seconds wall clock time: 63 minutes 4.32 seconds (3784.32 seconds total)