Starting phenix.real_space_refine on Wed Nov 15 13:22:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4u_24833/11_2023/7s4u_24833.pdb" } resolution = 3.56 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= 0.107 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 142 5.49 5 S 16 5.16 5 C 7078 2.51 5 N 2093 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 664": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 1078": "NH1" <-> "NH2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A ASP 1193": "OD1" <-> "OD2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A ARG 1279": "NH1" <-> "NH2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "A ARG 1303": "NH1" <-> "NH2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A GLU 1341": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11927 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8928 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 29, 'TRANS': 1062} Chain breaks: 7 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2080 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 48, 'rna3p_pyr': 32} Link IDs: {'rna2p': 17, 'rna3p': 79} Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 7.10, per 1000 atoms: 0.60 Number of scatterers: 11927 At special positions: 0 Unit cell: (89.1, 130.9, 145.2, 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 16 16.00 P 142 15.00 O 2598 8.00 N 2093 7.00 C 7078 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: 6.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 5 sheets defined 58.2% alpha, 8.4% beta 38 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 3.794A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.572A pdb=" N LEU A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.612A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.653A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.547A pdb=" N SER A 179 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.597A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 237 through 246 removed outlier: 4.775A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.697A pdb=" N ASP A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.649A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 removed outlier: 4.112A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.537A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.722A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (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: 3.698A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.278A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.009A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.567A pdb=" N ASN A 477 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 478 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.920A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.514A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 removed outlier: 4.188A pdb=" N ASP A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.720A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.524A pdb=" N ARG A 691 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.917A pdb=" N HIS A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 5.729A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.850A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.572A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.266A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1076 through 1089 removed outlier: 4.189A pdb=" N PHE A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR A1082 " --> pdb=" O ARG A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.532A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.585A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1238 " --> pdb=" O ASN A1234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1260 removed outlier: 4.191A pdb=" N GLN A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.883A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1338 through 1343 removed outlier: 3.605A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.397A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 18 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.655A pdb=" N LYS A 30 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.938A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A1109 " --> pdb=" O ASP A1135 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1133 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.667A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326 385 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2410 1.33 - 1.45: 3417 1.45 - 1.57: 6303 1.57 - 1.69: 281 1.69 - 1.81: 31 Bond restraints: 12442 Sorted by residual: bond pdb=" N ASP A 686 " pdb=" CA ASP A 686 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.31e-02 5.83e+03 5.27e+00 bond pdb=" CA LYS A 348 " pdb=" C LYS A 348 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.77e+00 bond pdb=" CA GLY A1165 " pdb=" C GLY A1165 " ideal model delta sigma weight residual 1.518 1.529 -0.011 7.30e-03 1.88e+04 2.14e+00 bond pdb=" C SER A 685 " pdb=" N ASP A 686 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.37e-02 5.33e+03 2.12e+00 bond pdb=" CA ILE A 448 " pdb=" C ILE A 448 " ideal model delta sigma weight residual 1.527 1.515 0.011 8.00e-03 1.56e+04 2.01e+00 ... (remaining 12437 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.69: 816 105.69 - 112.77: 6731 112.77 - 119.86: 4372 119.86 - 126.95: 5061 126.95 - 134.03: 433 Bond angle restraints: 17413 Sorted by residual: angle pdb=" C3' C B 90 " pdb=" O3' C B 90 " pdb=" P G B 91 " ideal model delta sigma weight residual 120.20 126.48 -6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" C3' C B 2 " pdb=" O3' C B 2 " pdb=" P G B 3 " ideal model delta sigma weight residual 120.20 125.75 -5.55 1.50e+00 4.44e-01 1.37e+01 angle pdb=" O3' C B 90 " pdb=" C3' C B 90 " pdb=" C2' C B 90 " ideal model delta sigma weight residual 113.70 119.04 -5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C2' G B 3 " pdb=" C1' G B 3 " pdb=" N9 G B 3 " ideal model delta sigma weight residual 112.00 117.12 -5.12 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N ILE A 615 " pdb=" CA ILE A 615 " pdb=" C ILE A 615 " ideal model delta sigma weight residual 111.45 108.31 3.14 9.30e-01 1.16e+00 1.14e+01 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6892 35.30 - 70.60: 268 70.60 - 105.90: 25 105.90 - 141.20: 4 141.20 - 176.49: 4 Dihedral angle restraints: 7193 sinusoidal: 3981 harmonic: 3212 Sorted by residual: dihedral pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" C2' A B 1 " pdb=" C1' A B 1 " ideal model delta sinusoidal sigma weight residual -35.00 34.21 -69.21 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C5' A B 1 " pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" O3' A B 1 " ideal model delta sinusoidal sigma weight residual 147.00 82.33 64.67 1 8.00e+00 1.56e-02 8.58e+01 dihedral pdb=" O4' C B 69 " pdb=" C1' C B 69 " pdb=" N1 C B 69 " pdb=" C2 C B 69 " ideal model delta sinusoidal sigma weight residual 200.00 50.22 149.78 1 1.50e+01 4.44e-03 7.95e+01 ... (remaining 7190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1794 0.065 - 0.129: 212 0.129 - 0.194: 13 0.194 - 0.259: 2 0.259 - 0.324: 1 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C3' A B 1 " pdb=" C4' A B 1 " pdb=" O3' A B 1 " pdb=" C2' A B 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1' G B 3 " pdb=" O4' G B 3 " pdb=" C2' G B 3 " pdb=" N9 G B 3 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C2' A B 1 " pdb=" C3' A B 1 " pdb=" O2' A B 1 " pdb=" C1' A B 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2019 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.036 2.00e-02 2.50e+03 1.61e-02 7.78e+00 pdb=" N9 G B 3 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.028 2.00e-02 2.50e+03 1.30e-02 4.66e+00 pdb=" N9 A B 7 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 7 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A B 7 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 35 " 0.028 2.00e-02 2.50e+03 1.18e-02 4.16e+00 pdb=" N9 DG C 35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG C 35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG C 35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG C 35 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG C 35 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG C 35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG C 35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG C 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG C 35 " -0.003 2.00e-02 2.50e+03 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 251 2.65 - 3.21: 10971 3.21 - 3.78: 18440 3.78 - 4.34: 25014 4.34 - 4.90: 38258 Nonbonded interactions: 92934 Sorted by model distance: nonbonded pdb=" O2' C B 90 " pdb=" OP1 G B 91 " model vdw 2.090 2.440 nonbonded pdb=" OG SER A 541 " pdb=" OD2 ASP A 686 " model vdw 2.105 2.440 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.159 2.440 nonbonded pdb=" O2' A B 37 " pdb=" OP1 G B 38 " model vdw 2.200 2.440 ... (remaining 92929 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=0.00 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 12.470 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 0.033 12442 Z= 0.246 Angle : 0.737 9.851 17413 Z= 0.413 Chirality : 0.042 0.324 2022 Planarity : 0.004 0.042 1694 Dihedral : 17.279 176.495 5107 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.09 (0.25), residues: 1076 helix: -0.75 (0.22), residues: 517 sheet: -0.15 (0.52), residues: 106 loop : -0.61 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2989 time to fit residues: 33.5228 Evaluate side-chains 47 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12442 Z= 0.163 Angle : 0.597 8.409 17413 Z= 0.318 Chirality : 0.039 0.236 2022 Planarity : 0.004 0.036 1694 Dihedral : 17.848 176.818 2791 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.51 % Allowed : 3.88 % Favored : 95.61 % 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: -0.56 (0.26), residues: 1076 helix: -0.20 (0.22), residues: 529 sheet: -0.24 (0.52), residues: 106 loop : -0.41 (0.30), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 0.3514 time to fit residues: 30.9591 Evaluate side-chains 51 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1207 time to fit residues: 2.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12442 Z= 0.288 Angle : 0.659 10.007 17413 Z= 0.347 Chirality : 0.041 0.242 2022 Planarity : 0.004 0.038 1694 Dihedral : 17.900 179.220 2791 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 5.51 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1076 helix: -0.28 (0.22), residues: 532 sheet: -0.36 (0.53), residues: 106 loop : -0.89 (0.29), residues: 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.2938 time to fit residues: 24.3132 Evaluate side-chains 49 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1104 time to fit residues: 2.4962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12442 Z= 0.208 Angle : 0.585 9.050 17413 Z= 0.309 Chirality : 0.038 0.185 2022 Planarity : 0.003 0.038 1694 Dihedral : 17.699 179.578 2791 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % 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: -0.76 (0.25), residues: 1076 helix: -0.09 (0.22), residues: 532 sheet: -0.45 (0.53), residues: 108 loop : -0.89 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.3069 time to fit residues: 24.0717 Evaluate side-chains 51 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1022 time to fit residues: 1.6883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12442 Z= 0.279 Angle : 0.624 9.515 17413 Z= 0.329 Chirality : 0.040 0.195 2022 Planarity : 0.004 0.039 1694 Dihedral : 17.739 178.038 2791 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.82 % Allowed : 8.98 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1076 helix: -0.06 (0.22), residues: 523 sheet: -0.53 (0.52), residues: 106 loop : -0.94 (0.29), residues: 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.3118 time to fit residues: 26.7087 Evaluate side-chains 55 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1361 time to fit residues: 2.0904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12442 Z= 0.317 Angle : 0.654 9.529 17413 Z= 0.343 Chirality : 0.041 0.198 2022 Planarity : 0.004 0.043 1694 Dihedral : 17.783 176.872 2791 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.02 % Allowed : 10.20 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.25), residues: 1076 helix: -0.17 (0.22), residues: 529 sheet: -0.74 (0.52), residues: 106 loop : -1.17 (0.29), residues: 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 1.186 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.2894 time to fit residues: 26.4811 Evaluate side-chains 56 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1151 time to fit residues: 2.6868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 0.0030 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12442 Z= 0.146 Angle : 0.537 9.326 17413 Z= 0.283 Chirality : 0.036 0.177 2022 Planarity : 0.003 0.045 1694 Dihedral : 17.506 178.044 2791 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.20 % Allowed : 11.12 % Favored : 88.67 % 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 (0.26), residues: 1076 helix: 0.24 (0.23), residues: 526 sheet: -0.40 (0.54), residues: 95 loop : -1.01 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.3350 time to fit residues: 27.3212 Evaluate side-chains 53 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1282 time to fit residues: 1.7326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12442 Z= 0.253 Angle : 0.603 9.034 17413 Z= 0.316 Chirality : 0.039 0.193 2022 Planarity : 0.004 0.044 1694 Dihedral : 17.563 179.622 2791 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.10 % Allowed : 11.63 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1076 helix: 0.07 (0.23), residues: 527 sheet: -0.47 (0.53), residues: 94 loop : -1.15 (0.28), residues: 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.181 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.3303 time to fit residues: 25.6008 Evaluate side-chains 52 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 0.0980 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12442 Z= 0.163 Angle : 0.540 8.360 17413 Z= 0.284 Chirality : 0.037 0.206 2022 Planarity : 0.003 0.050 1694 Dihedral : 17.378 178.115 2791 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.20 % Allowed : 11.94 % Favored : 87.86 % 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 (0.26), residues: 1076 helix: 0.27 (0.23), residues: 527 sheet: -0.50 (0.53), residues: 95 loop : -1.04 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.237 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.3611 time to fit residues: 27.3941 Evaluate side-chains 54 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1289 time to fit residues: 1.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12442 Z= 0.175 Angle : 0.547 11.819 17413 Z= 0.287 Chirality : 0.037 0.198 2022 Planarity : 0.003 0.049 1694 Dihedral : 17.267 178.038 2791 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.10 % Allowed : 11.84 % Favored : 88.06 % 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 (0.25), residues: 1076 helix: 0.26 (0.23), residues: 529 sheet: -0.49 (0.53), residues: 95 loop : -1.02 (0.29), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.212 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.3605 time to fit residues: 26.3050 Evaluate side-chains 53 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1074 time to fit residues: 1.8152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.133234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100789 restraints weight = 22853.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103028 restraints weight = 48121.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.103546 restraints weight = 23828.598| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12442 Z= 0.186 Angle : 0.551 12.118 17413 Z= 0.290 Chirality : 0.037 0.202 2022 Planarity : 0.003 0.050 1694 Dihedral : 17.211 178.219 2791 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.10 % Allowed : 12.24 % Favored : 87.65 % 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: -0.53 (0.26), residues: 1076 helix: 0.30 (0.23), residues: 528 sheet: -0.49 (0.52), residues: 95 loop : -1.01 (0.29), residues: 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.17 seconds wall clock time: 36 minutes 23.27 seconds (2183.27 seconds total)