Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 16:39:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynd_33959/04_2023/7ynd_33959.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 38 5.49 5 S 76 5.16 5 C 11305 2.51 5 N 3222 2.21 5 O 3457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 994": "NH1" <-> "NH2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A PHE 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A ARG 1260": "NH1" <-> "NH2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A GLU 1281": "OE1" <-> "OE2" Residue "A GLU 1318": "OE1" <-> "OE2" Residue "A GLU 1330": "OE1" <-> "OE2" Residue "A ARG 1356": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A GLU 1518": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1567, 12683 Classifications: {'peptide': 1567} Link IDs: {'PTRANS': 85, 'TRANS': 1481} Chain breaks: 2 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 5, 'rna3p_pur': 6, 'rna3p_pyr': 12} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4605 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Time building chain proxies: 10.43, per 1000 atoms: 0.58 Number of scatterers: 18098 At special positions: 0 Unit cell: (130.54, 199.02, 130.54, 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 76 16.00 P 38 15.00 O 3457 8.00 N 3222 7.00 C 11305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 711 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 23 sheets defined 32.3% alpha, 15.3% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.749A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.702A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 294 through 299 removed outlier: 7.111A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 344 through 365 removed outlier: 3.711A pdb=" N TRP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.668A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.667A pdb=" N ARG A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.518A pdb=" N LYS A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 585 through 593 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.736A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.642A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 786 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.676A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.204A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.691A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1304 removed outlier: 3.563A pdb=" N LYS A1303 " --> pdb=" O MET A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.890A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1335 removed outlier: 3.623A pdb=" N LEU A1335 " --> pdb=" O ARG A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.812A pdb=" N LEU A1347 " --> pdb=" O PRO A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1425 removed outlier: 3.756A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 removed outlier: 3.773A pdb=" N LEU A1468 " --> pdb=" O LYS A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.763A pdb=" N GLY A1492 " --> pdb=" O LYS A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 3.952A pdb=" N GLY A1524 " --> pdb=" O PRO A1520 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A1534 " --> pdb=" O LEU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1548 Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.640A pdb=" N LEU A1579 " --> pdb=" O GLY A1575 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1580 " --> pdb=" O TYR A1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1575 through 1580' Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.624A pdb=" N GLN C 9 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.978A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.645A pdb=" N THR C 44 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 75 through 89 removed outlier: 4.145A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 108 removed outlier: 4.091A pdb=" N ARG C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 143 through 161 removed outlier: 3.837A pdb=" N VAL C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 183 removed outlier: 3.867A pdb=" N ARG C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.512A pdb=" N LYS C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.849A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.815A pdb=" N GLN C 232 " --> pdb=" O MET C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.795A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.661A pdb=" N TYR C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 Processing helix chain 'C' and resid 297 through 310 removed outlier: 3.846A pdb=" N ILE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 360 through 374 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.803A pdb=" N ILE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.517A pdb=" N ARG C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU C 419 " --> pdb=" O PHE C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 432 through 437 removed outlier: 3.863A pdb=" N GLU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.692A pdb=" N ILE C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.927A pdb=" N VAL C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.816A pdb=" N PHE C 504 " --> pdb=" O PRO C 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 505 " --> pdb=" O PHE C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.813A pdb=" N LEU C 523 " --> pdb=" O HIS C 520 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 526' Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.702A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 558 " --> pdb=" O TRP C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 554 through 558' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.049A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.408A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.408A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.725A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 724 Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AB1, first strand: chain 'A' and resid 739 through 742 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.608A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 6.999A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A1495 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 993 through 995 removed outlier: 6.751A pdb=" N GLU A1226 " --> pdb=" O LYS A1004 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 9.032A pdb=" N THR A1008 " --> pdb=" O GLN A1127 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086 Processing sheet with id=AB9, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AC1, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.706A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1276 through 1280 removed outlier: 6.719A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1385 through 1387 Processing sheet with id=AC4, first strand: chain 'C' and resid 314 through 315 Processing sheet with id=AC5, first strand: chain 'C' and resid 457 through 462 removed outlier: 6.416A pdb=" N ILE C 424 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 518 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 426 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 550 " --> pdb=" O VAL C 515 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 7.98 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: 5666 1.33 - 1.46: 3873 1.46 - 1.58: 8878 1.58 - 1.70: 75 1.70 - 1.83: 111 Bond restraints: 18603 Sorted by residual: bond pdb=" N VAL A 842 " pdb=" CA VAL A 842 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.53e+00 bond pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.22e-02 6.72e+03 8.36e+00 bond pdb=" N GLN A1056 " pdb=" CA GLN A1056 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.09e+00 bond pdb=" N ASP A 838 " pdb=" CA ASP A 838 " ideal model delta sigma weight residual 1.452 1.488 -0.037 1.30e-02 5.92e+03 8.01e+00 bond pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.62e+00 ... (remaining 18598 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.67: 759 106.67 - 113.77: 10167 113.77 - 120.87: 8564 120.87 - 127.97: 5531 127.97 - 135.06: 221 Bond angle restraints: 25242 Sorted by residual: angle pdb=" N TYR A 866 " pdb=" CA TYR A 866 " pdb=" C TYR A 866 " ideal model delta sigma weight residual 111.02 117.62 -6.60 1.25e+00 6.40e-01 2.79e+01 angle pdb=" C GLU A 633 " pdb=" N MET A 634 " pdb=" CA MET A 634 " ideal model delta sigma weight residual 121.54 112.85 8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASP A 841 " pdb=" CA ASP A 841 " pdb=" CB ASP A 841 " ideal model delta sigma weight residual 111.26 118.60 -7.34 1.67e+00 3.59e-01 1.93e+01 angle pdb=" N ASP A 649 " pdb=" CA ASP A 649 " pdb=" C ASP A 649 " ideal model delta sigma weight residual 110.24 115.73 -5.49 1.30e+00 5.92e-01 1.78e+01 angle pdb=" C GLU A1392 " pdb=" N ARG A1393 " pdb=" CA ARG A1393 " ideal model delta sigma weight residual 121.80 131.79 -9.99 2.44e+00 1.68e-01 1.68e+01 ... (remaining 25237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 10845 35.62 - 71.24: 353 71.24 - 106.86: 20 106.86 - 142.48: 0 142.48 - 178.10: 3 Dihedral angle restraints: 11221 sinusoidal: 5082 harmonic: 6139 Sorted by residual: dihedral pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " pdb=" C2 U B 21 " ideal model delta sinusoidal sigma weight residual -160.00 18.10 -178.10 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" CA GLU A 633 " pdb=" C GLU A 633 " pdb=" N MET A 634 " pdb=" CA MET A 634 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 11218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2209 0.065 - 0.130: 388 0.130 - 0.195: 34 0.195 - 0.260: 2 0.260 - 0.325: 2 Chirality restraints: 2635 Sorted by residual: chirality pdb=" CA ASP A 841 " pdb=" N ASP A 841 " pdb=" C ASP A 841 " pdb=" CB ASP A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE A 376 " pdb=" CA ILE A 376 " pdb=" CG1 ILE A 376 " pdb=" CG2 ILE A 376 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" C PRO A 864 " pdb=" CB PRO A 864 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2632 not shown) Planarity restraints: 3169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 864 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 768 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A 769 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO A 904 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.035 5.00e-02 4.00e+02 ... (remaining 3166 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2892 2.75 - 3.29: 15852 3.29 - 3.83: 27936 3.83 - 4.36: 32550 4.36 - 4.90: 57742 Nonbonded interactions: 136972 Sorted by model distance: nonbonded pdb=" O2' A B 13 " pdb=" OP1 A B 14 " model vdw 2.213 2.440 nonbonded pdb=" NZ LYS A 304 " pdb=" OD1 ASP A 310 " model vdw 2.219 2.520 nonbonded pdb=" O ARG A 489 " pdb=" OG SER A 490 " model vdw 2.225 2.440 nonbonded pdb=" OE2 GLU A1226 " pdb=" OH TYR A1228 " model vdw 2.234 2.440 nonbonded pdb=" O GLN C 421 " pdb=" NH2 ARG C 513 " model vdw 2.235 2.520 ... (remaining 136967 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: 4.810 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: 0.020 Extract box with map and model: 12.260 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 53.380 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.007 0.043 18603 Z= 0.437 Angle : 0.785 10.063 25242 Z= 0.458 Chirality : 0.049 0.325 2635 Planarity : 0.006 0.084 3169 Dihedral : 17.060 178.105 7251 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.55 % Favored : 89.22 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.14), residues: 2105 helix: -1.85 (0.18), residues: 591 sheet: -1.64 (0.28), residues: 297 loop : -3.85 (0.13), residues: 1217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 2.035 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.3742 time to fit residues: 87.8071 Evaluate side-chains 109 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2059 time to fit residues: 8.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 260 ASN A 276 ASN A 456 GLN A 493 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 ASN A1419 HIS A1428 ASN A1483 HIS ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 436 HIS C 477 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18603 Z= 0.241 Angle : 0.623 12.197 25242 Z= 0.327 Chirality : 0.044 0.207 2635 Planarity : 0.005 0.074 3169 Dihedral : 10.314 179.013 2785 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer Outliers : 1.78 % 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: -3.16 (0.16), residues: 2105 helix: -0.37 (0.21), residues: 617 sheet: -1.14 (0.28), residues: 294 loop : -3.51 (0.14), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 2.039 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 128 average time/residue: 0.3572 time to fit residues: 69.3114 Evaluate side-chains 104 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2167 time to fit residues: 8.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 18603 Z= 0.237 Angle : 0.599 10.436 25242 Z= 0.312 Chirality : 0.043 0.186 2635 Planarity : 0.005 0.067 3169 Dihedral : 10.237 178.265 2785 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.17), residues: 2105 helix: 0.48 (0.22), residues: 607 sheet: -0.87 (0.28), residues: 303 loop : -3.30 (0.15), residues: 1195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 2.080 Fit side-chains outliers start: 30 outliers final: 7 residues processed: 127 average time/residue: 0.3520 time to fit residues: 67.8582 Evaluate side-chains 99 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1887 time to fit residues: 5.3629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.0770 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 18603 Z= 0.372 Angle : 0.664 10.806 25242 Z= 0.346 Chirality : 0.046 0.190 2635 Planarity : 0.005 0.076 3169 Dihedral : 10.363 177.514 2785 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer Outliers : 2.27 % 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: -2.38 (0.18), residues: 2105 helix: 0.63 (0.22), residues: 615 sheet: -0.69 (0.29), residues: 305 loop : -3.25 (0.15), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 92 time to evaluate : 2.414 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 128 average time/residue: 0.3296 time to fit residues: 65.4262 Evaluate side-chains 116 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1728 time to fit residues: 11.8729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN C 81 GLN C 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 18603 Z= 0.393 Angle : 0.679 11.541 25242 Z= 0.352 Chirality : 0.047 0.199 2635 Planarity : 0.005 0.077 3169 Dihedral : 10.413 177.567 2785 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.18), residues: 2105 helix: 0.66 (0.22), residues: 619 sheet: -0.60 (0.29), residues: 305 loop : -3.21 (0.15), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 2.212 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 112 average time/residue: 0.3604 time to fit residues: 61.7344 Evaluate side-chains 99 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2162 time to fit residues: 7.5994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 18603 Z= 0.231 Angle : 0.601 11.150 25242 Z= 0.311 Chirality : 0.044 0.188 2635 Planarity : 0.005 0.072 3169 Dihedral : 10.235 178.000 2785 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer Outliers : 0.86 % 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: -2.04 (0.18), residues: 2105 helix: 0.97 (0.22), residues: 614 sheet: -0.44 (0.29), residues: 303 loop : -3.09 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 2.173 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 109 average time/residue: 0.3578 time to fit residues: 59.5664 Evaluate side-chains 94 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1868 time to fit residues: 4.9220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 125 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1405 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 18603 Z= 0.302 Angle : 0.632 11.018 25242 Z= 0.326 Chirality : 0.045 0.201 2635 Planarity : 0.005 0.071 3169 Dihedral : 10.247 177.831 2785 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 2105 helix: 1.03 (0.22), residues: 614 sheet: -0.39 (0.29), residues: 303 loop : -3.09 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 2.008 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 103 average time/residue: 0.3557 time to fit residues: 56.5375 Evaluate side-chains 95 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1982 time to fit residues: 5.0857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 18603 Z= 0.427 Angle : 0.699 11.199 25242 Z= 0.362 Chirality : 0.048 0.204 2635 Planarity : 0.005 0.074 3169 Dihedral : 10.410 177.380 2785 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.18), residues: 2105 helix: 0.85 (0.22), residues: 621 sheet: -0.41 (0.29), residues: 303 loop : -3.14 (0.16), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 2.117 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 0.3483 time to fit residues: 58.3840 Evaluate side-chains 100 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1807 time to fit residues: 6.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.2980 chunk 196 optimal weight: 0.0570 chunk 179 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1337 HIS A1405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 18603 Z= 0.160 Angle : 0.577 10.426 25242 Z= 0.297 Chirality : 0.042 0.196 2635 Planarity : 0.004 0.071 3169 Dihedral : 10.077 179.467 2785 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.76 (0.18), residues: 2105 helix: 1.25 (0.22), residues: 614 sheet: -0.29 (0.30), residues: 307 loop : -2.95 (0.16), residues: 1184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 2.470 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 103 average time/residue: 0.3953 time to fit residues: 60.8964 Evaluate side-chains 93 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2351 time to fit residues: 3.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.4980 chunk 202 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18603 Z= 0.196 Angle : 0.583 10.700 25242 Z= 0.301 Chirality : 0.043 0.180 2635 Planarity : 0.004 0.067 3169 Dihedral : 10.004 178.961 2785 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.64 (0.18), residues: 2105 helix: 1.37 (0.22), residues: 614 sheet: -0.21 (0.30), residues: 307 loop : -2.89 (0.16), residues: 1184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 2.066 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.3700 time to fit residues: 56.0903 Evaluate side-chains 95 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1855 time to fit residues: 3.7634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.4980 chunk 180 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075395 restraints weight = 35549.627| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.52 r_work: 0.2864 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18603 Z= 0.195 Angle : 0.578 10.455 25242 Z= 0.298 Chirality : 0.042 0.176 2635 Planarity : 0.004 0.069 3169 Dihedral : 9.950 179.057 2785 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.55 (0.18), residues: 2105 helix: 1.46 (0.22), residues: 614 sheet: -0.12 (0.30), residues: 300 loop : -2.84 (0.16), residues: 1191 =============================================================================== Job complete usr+sys time: 3414.67 seconds wall clock time: 63 minutes 6.13 seconds (3786.13 seconds total)