Starting phenix.real_space_refine on Sun Feb 25 12:15:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8j_27249/02_2024/8d8j_27249_neut_updated.pdb" } resolution = 3.8 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= 0.028 sd= 1.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 1183 5.49 5 Mg 29 5.21 5 S 98 5.16 5 C 27929 2.51 5 N 9221 2.21 5 O 12922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ASP 49": "OD1" <-> "OD2" Residue "5 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 275": "OE1" <-> "OE2" Residue "5 ASP 286": "OD1" <-> "OD2" Residue "5 GLU 296": "OE1" <-> "OE2" Residue "5 GLU 310": "OE1" <-> "OE2" Residue "5 TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 241": "OD1" <-> "OD2" Residue "d ASP 245": "OD1" <-> "OD2" Residue "d GLU 253": "OE1" <-> "OE2" Residue "d GLU 266": "OE1" <-> "OE2" Residue "d GLU 267": "OE1" <-> "OE2" Residue "d PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 431": "OE1" <-> "OE2" Residue "d TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 460": "OE1" <-> "OE2" Residue "d ASP 513": "OD1" <-> "OD2" Residue "d GLU 524": "OE1" <-> "OE2" Residue "d PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 538": "OD1" <-> "OD2" Residue "d PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 561": "OD1" <-> "OD2" Residue "d GLU 565": "OE1" <-> "OE2" Residue "d GLU 613": "OE1" <-> "OE2" Residue "d PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 634": "OE1" <-> "OE2" Residue "d GLU 661": "OE1" <-> "OE2" Residue "d PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 737": "OD1" <-> "OD2" Residue "d GLU 754": "OE1" <-> "OE2" Residue "d ASP 785": "OD1" <-> "OD2" Residue "d ASP 804": "OD1" <-> "OD2" Residue "O PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 111": "OE1" <-> "OE2" Residue "O PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 98": "OD1" <-> "OD2" Residue "P PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 127": "OD1" <-> "OD2" Residue "R PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "V ASP 150": "OD1" <-> "OD2" Residue "V ASP 157": "OD1" <-> "OD2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 213": "OE1" <-> "OE2" Residue "2 ASP 36": "OD1" <-> "OD2" Residue "2 ASP 40": "OD1" <-> "OD2" Residue "2 GLU 114": "OE1" <-> "OE2" Residue "2 GLU 127": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 287": "OD1" <-> "OD2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "6 GLU 99": "OE1" <-> "OE2" Residue "6 ASP 112": "OD1" <-> "OD2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L ASP 117": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51386 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 2448 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 436} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 3 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1660 Unresolved non-hydrogen angles: 2098 Unresolved non-hydrogen dihedrals: 1399 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 16, 'TYR:plan': 16, 'ASN:plan1': 36, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 927 Chain: "5" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2199 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 13, 'TRANS': 256} Chain breaks: 2 Chain: "d" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5497 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 15, 'TRANS': 644} Chain breaks: 3 Chain: "O" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1724 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain breaks: 1 Chain: "Q" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1172 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 2 Chain: "R" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 454 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "V" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1787 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain: "2" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 833 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2567 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 22, 'TRANS': 285} Chain breaks: 2 Chain: "E" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1334 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain: "F" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "6" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2063 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 18, 'TRANS': 231} Chain breaks: 1 Chain: "H" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1221 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "a" Number of atoms: 25157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 25157 Classifications: {'RNA': 1183} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 58, 'rna3p_pur': 562, 'rna3p_pyr': 460} Link IDs: {'rna2p': 161, 'rna3p': 1021} Chain breaks: 21 Chain: "L" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 112} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' MG': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1393 SG CYS 0 400 58.631 70.164 81.703 1.00 49.72 S ATOM 1254 SG CYS 0 373 56.072 68.870 87.415 1.00 47.30 S ATOM 1878 SG CYS 0 513 59.075 64.201 84.813 1.00 47.97 S ATOM 1287 SG CYS 0 379 62.106 69.702 86.849 1.00 51.34 S Time building chain proxies: 25.78, per 1000 atoms: 0.50 Number of scatterers: 51386 At special positions: 0 Unit cell: (179.69, 228.312, 275.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 98 16.00 P 1183 15.00 Mg 29 11.99 O 12922 8.00 N 9221 7.00 C 27929 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: 27.70 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 701 " pdb="FE2 SF4 0 701 " - pdb=" SG CYS 0 373 " pdb="FE4 SF4 0 701 " - pdb=" SG CYS 0 379 " pdb="FE1 SF4 0 701 " - pdb=" SG CYS 0 400 " pdb="FE3 SF4 0 701 " - pdb=" SG CYS 0 513 " Number of angles added : 12 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6482 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 17 sheets defined 49.3% alpha, 8.1% beta 378 base pairs and 638 stacking pairs defined. Time for finding SS restraints: 26.92 Creating SS restraints... Processing helix chain '0' and resid 66 through 71 Processing helix chain '0' and resid 82 through 91 Processing helix chain '0' and resid 98 through 112 removed outlier: 3.664A pdb=" N ILE 0 112 " --> pdb=" O TYR 0 108 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 154 removed outlier: 3.891A pdb=" N PHE 0 136 " --> pdb=" O ILE 0 132 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU 0 137 " --> pdb=" O ALA 0 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN 0 138 " --> pdb=" O SER 0 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY 0 141 " --> pdb=" O LEU 0 137 " (cutoff:3.500A) Processing helix chain '0' and resid 173 through 182 Processing helix chain '0' and resid 199 through 211 removed outlier: 3.983A pdb=" N GLU 0 203 " --> pdb=" O ALA 0 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG 0 204 " --> pdb=" O GLU 0 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG 0 211 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) Processing helix chain '0' and resid 285 through 299 removed outlier: 3.914A pdb=" N VAL 0 289 " --> pdb=" O PHE 0 285 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP 0 290 " --> pdb=" O PRO 0 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN 0 298 " --> pdb=" O GLU 0 294 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE 0 299 " --> pdb=" O HIS 0 295 " (cutoff:3.500A) Processing helix chain '0' and resid 314 through 328 Processing helix chain '0' and resid 330 through 333 Processing helix chain '0' and resid 386 through 390 Processing helix chain '0' and resid 410 through 415 Processing helix chain '0' and resid 465 through 475 Processing helix chain '0' and resid 491 through 493 No H-bonds generated for 'chain '0' and resid 491 through 493' Processing helix chain '0' and resid 531 through 538 Processing helix chain '0' and resid 560 through 598 removed outlier: 3.797A pdb=" N LYS 0 576 " --> pdb=" O ILE 0 572 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS 0 577 " --> pdb=" O LYS 0 573 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 0 579 " --> pdb=" O LEU 0 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG 0 580 " --> pdb=" O LYS 0 576 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 0 584 " --> pdb=" O ARG 0 580 " (cutoff:3.500A) Processing helix chain '0' and resid 606 through 627 removed outlier: 3.546A pdb=" N ARG 0 627 " --> pdb=" O GLN 0 623 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 56 Processing helix chain '5' and resid 62 through 66 Processing helix chain '5' and resid 69 through 76 removed outlier: 4.261A pdb=" N GLN 5 72 " --> pdb=" O LYS 5 69 " (cutoff:3.500A) Processing helix chain '5' and resid 99 through 103 Processing helix chain '5' and resid 116 through 124 Processing helix chain '5' and resid 131 through 136 Processing helix chain '5' and resid 139 through 151 removed outlier: 3.617A pdb=" N PHE 5 150 " --> pdb=" O LEU 5 146 " (cutoff:3.500A) Processing helix chain '5' and resid 156 through 172 removed outlier: 4.573A pdb=" N HIS 5 168 " --> pdb=" O TYR 5 164 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS 5 169 " --> pdb=" O GLY 5 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU 5 171 " --> pdb=" O GLU 5 167 " (cutoff:3.500A) Processing helix chain '5' and resid 176 through 178 No H-bonds generated for 'chain '5' and resid 176 through 178' Processing helix chain '5' and resid 184 through 198 Processing helix chain '5' and resid 204 through 217 removed outlier: 3.770A pdb=" N LYS 5 216 " --> pdb=" O GLN 5 212 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 239 Processing helix chain '5' and resid 264 through 287 removed outlier: 4.892A pdb=" N GLY 5 276 " --> pdb=" O SER 5 272 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE 5 277 " --> pdb=" O LYS 5 273 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 326 removed outlier: 4.430A pdb=" N LEU 5 324 " --> pdb=" O LYS 5 320 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU 5 325 " --> pdb=" O ALA 5 321 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU 5 326 " --> pdb=" O LEU 5 322 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 152 No H-bonds generated for 'chain 'd' and resid 149 through 152' Processing helix chain 'd' and resid 163 through 171 Processing helix chain 'd' and resid 181 through 191 Processing helix chain 'd' and resid 197 through 210 Processing helix chain 'd' and resid 220 through 232 Processing helix chain 'd' and resid 246 through 269 Processing helix chain 'd' and resid 284 through 297 Processing helix chain 'd' and resid 300 through 314 Processing helix chain 'd' and resid 320 through 332 Processing helix chain 'd' and resid 336 through 349 Processing helix chain 'd' and resid 357 through 369 Processing helix chain 'd' and resid 373 through 385 Processing helix chain 'd' and resid 392 through 405 Processing helix chain 'd' and resid 409 through 412 No H-bonds generated for 'chain 'd' and resid 409 through 412' Processing helix chain 'd' and resid 416 through 432 Processing helix chain 'd' and resid 441 through 455 Processing helix chain 'd' and resid 459 through 479 Processing helix chain 'd' and resid 487 through 496 removed outlier: 4.561A pdb=" N ASP d 490 " --> pdb=" O VAL d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 499 through 510 Processing helix chain 'd' and resid 519 through 522 No H-bonds generated for 'chain 'd' and resid 519 through 522' Processing helix chain 'd' and resid 524 through 542 Processing helix chain 'd' and resid 565 through 580 Processing helix chain 'd' and resid 593 through 613 removed outlier: 4.157A pdb=" N GLN d 612 " --> pdb=" O ASP d 608 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU d 613 " --> pdb=" O SER d 609 " (cutoff:3.500A) Processing helix chain 'd' and resid 617 through 635 Processing helix chain 'd' and resid 643 through 656 Proline residue: d 653 - end of helix Processing helix chain 'd' and resid 659 through 669 Processing helix chain 'd' and resid 673 through 688 Processing helix chain 'd' and resid 719 through 732 removed outlier: 4.721A pdb=" N ARG d 731 " --> pdb=" O ILE d 727 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N HIS d 732 " --> pdb=" O THR d 728 " (cutoff:3.500A) Processing helix chain 'd' and resid 738 through 751 Processing helix chain 'd' and resid 754 through 767 Processing helix chain 'd' and resid 771 through 775 Processing helix chain 'd' and resid 778 through 798 Processing helix chain 'd' and resid 802 through 811 Processing helix chain 'd' and resid 820 through 833 removed outlier: 5.477A pdb=" N ASN d 825 " --> pdb=" O SER d 821 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU d 826 " --> pdb=" O MET d 822 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE d 833 " --> pdb=" O ALA d 829 " (cutoff:3.500A) Processing helix chain 'd' and resid 836 through 847 Processing helix chain 'O' and resid 35 through 58 Processing helix chain 'O' and resid 74 through 84 removed outlier: 3.709A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS O 84 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 110 removed outlier: 3.547A pdb=" N LYS O 109 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG O 110 " --> pdb=" O GLU O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 Processing helix chain 'O' and resid 149 through 164 Processing helix chain 'O' and resid 174 through 194 Processing helix chain 'O' and resid 199 through 222 Processing helix chain 'O' and resid 224 through 234 Processing helix chain 'O' and resid 238 through 242 Processing helix chain 'O' and resid 249 through 255 Processing helix chain 'P' and resid 52 through 57 removed outlier: 3.505A pdb=" N LYS P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'Q' and resid 81 through 116 removed outlier: 4.266A pdb=" N LEU Q 94 " --> pdb=" O SER Q 90 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU Q 99 " --> pdb=" O SER Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 134 Processing helix chain 'Q' and resid 171 through 182 Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 96 through 102 removed outlier: 3.782A pdb=" N TYR R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 115 No H-bonds generated for 'chain 'R' and resid 112 through 115' Processing helix chain 'R' and resid 119 through 135 Processing helix chain 'V' and resid 4 through 8 Processing helix chain 'V' and resid 30 through 36 Processing helix chain 'V' and resid 71 through 77 Processing helix chain 'V' and resid 91 through 148 removed outlier: 4.086A pdb=" N VAL V 95 " --> pdb=" O SER V 91 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS V 134 " --> pdb=" O LYS V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 161 removed outlier: 3.507A pdb=" N MET V 160 " --> pdb=" O LEU V 156 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER V 161 " --> pdb=" O ASP V 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 156 through 161' Processing helix chain 'V' and resid 170 through 207 removed outlier: 4.422A pdb=" N ASN V 207 " --> pdb=" O TYR V 203 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 222 removed outlier: 3.530A pdb=" N LYS V 218 " --> pdb=" O SER V 214 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 48 Processing helix chain '2' and resid 52 through 59 removed outlier: 3.748A pdb=" N LYS 2 56 " --> pdb=" O ASN 2 53 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP 2 57 " --> pdb=" O GLU 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 66 No H-bonds generated for 'chain '2' and resid 63 through 66' Processing helix chain '2' and resid 71 through 76 Processing helix chain '2' and resid 81 through 95 Processing helix chain '2' and resid 114 through 126 removed outlier: 4.570A pdb=" N LYS 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA 2 119 " --> pdb=" O ARG 2 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.622A pdb=" N TYR D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.680A pdb=" N THR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 removed outlier: 4.229A pdb=" N PHE D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 103 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 168 through 191 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.610A pdb=" N ALA D 377 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 471 through 483 removed outlier: 3.612A pdb=" N ARG D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 No H-bonds generated for 'chain 'E' and resid 140 through 143' Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 244 through 253 Processing helix chain 'E' and resid 268 through 280 Processing helix chain 'E' and resid 286 through 292 Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'F' and resid 17 through 34 removed outlier: 3.995A pdb=" N GLU F 20 " --> pdb=" O PRO F 17 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 33 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 87 Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 90 through 93 No H-bonds generated for 'chain '6' and resid 90 through 93' Processing helix chain '6' and resid 123 through 126 No H-bonds generated for 'chain '6' and resid 123 through 126' Processing helix chain '6' and resid 132 through 134 No H-bonds generated for 'chain '6' and resid 132 through 134' Processing helix chain '6' and resid 151 through 162 Processing helix chain '6' and resid 168 through 175 Processing helix chain '6' and resid 179 through 198 Processing helix chain '6' and resid 203 through 215 Processing helix chain 'H' and resid 3 through 18 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'L' and resid 31 through 36 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 142 through 145 No H-bonds generated for 'chain 'L' and resid 142 through 145' Processing sheet with id= A, first strand: chain '0' and resid 164 through 168 removed outlier: 6.528A pdb=" N LEU 0 271 " --> pdb=" O LEU 0 165 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL 0 167 " --> pdb=" O LEU 0 271 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE 0 273 " --> pdb=" O VAL 0 167 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N HIS 0 305 " --> pdb=" O ILE 0 272 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU 0 274 " --> pdb=" O HIS 0 305 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL 0 307 " --> pdb=" O LEU 0 274 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 191 through 194 Processing sheet with id= C, first strand: chain '0' and resid 402 through 407 Processing sheet with id= D, first strand: chain '0' and resid 502 through 504 removed outlier: 3.878A pdb=" N THR 0 551 " --> pdb=" O THR 0 523 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'P' and resid 6 through 15 removed outlier: 3.822A pdb=" N ARG P 15 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL P 25 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL P 39 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP P 64 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Q' and resid 72 through 74 removed outlier: 14.476A pdb=" N ASN Q 5 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU Q 7 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU Q 25 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS Q 21 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN Q 13 " --> pdb=" O THR Q 19 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR Q 19 " --> pdb=" O GLN Q 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Q' and resid 57 through 59 removed outlier: 6.614A pdb=" N ARG Q 59 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE Q 77 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= I, first strand: chain 'E' and resid 179 through 186 removed outlier: 3.812A pdb=" N ILE E 163 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 171 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY E 173 " --> pdb=" O MET E 146 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET E 146 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 220 through 224 Processing sheet with id= K, first strand: chain 'F' and resid 96 through 99 removed outlier: 4.008A pdb=" N LEU F 2 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 38 through 43 removed outlier: 6.604A pdb=" N LEU F 70 " --> pdb=" O ARG F 40 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 42 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU F 68 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '6' and resid 294 through 296 Processing sheet with id= N, first strand: chain '6' and resid 334 through 336 Processing sheet with id= O, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.587A pdb=" N SER H 47 " --> pdb=" O GLY H 76 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.859A pdb=" N LEU H 128 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG H 153 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU H 126 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 123 through 125 removed outlier: 6.778A pdb=" N ARG L 82 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL L 65 " --> pdb=" O ALA L 80 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA L 80 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL L 67 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG L 78 " --> pdb=" O VAL L 67 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 840 hydrogen bonds 1442 hydrogen bond angles 0 basepair planarities 378 basepair parallelities 638 stacking parallelities Total time for adding SS restraints: 35.85 Time building geometry restraints manager: 29.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 27061 1.43 - 1.65: 27590 1.65 - 1.87: 160 1.87 - 2.09: 0 2.09 - 2.31: 12 Bond restraints: 54823 Sorted by residual: bond pdb=" CG PHE d 218 " pdb=" CD2 PHE d 218 " ideal model delta sigma weight residual 1.384 1.336 0.048 2.10e-02 2.27e+03 5.13e+00 bond pdb=" S1 SF4 0 701 " pdb="FE2 SF4 0 701 " ideal model delta sigma weight residual 2.280 2.218 0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" S2 SF4 0 701 " pdb="FE1 SF4 0 701 " ideal model delta sigma weight residual 2.280 2.223 0.057 3.00e-02 1.11e+03 3.63e+00 bond pdb=" CA CYS H 152 " pdb=" CB CYS H 152 " ideal model delta sigma weight residual 1.533 1.503 0.029 1.82e-02 3.02e+03 2.61e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.57e+00 ... (remaining 54818 not shown) Histogram of bond angle deviations from ideal: 71.74 - 84.20: 12 84.20 - 96.67: 0 96.67 - 109.14: 16058 109.14 - 121.60: 50583 121.60 - 134.07: 13075 Bond angle restraints: 79728 Sorted by residual: angle pdb=" CG ARG R 124 " pdb=" CD ARG R 124 " pdb=" NE ARG R 124 " ideal model delta sigma weight residual 112.00 121.60 -9.60 2.20e+00 2.07e-01 1.90e+01 angle pdb=" C LEU 0 64 " pdb=" CA LEU 0 64 " pdb=" CB LEU 0 64 " ideal model delta sigma weight residual 117.23 112.04 5.19 1.36e+00 5.41e-01 1.45e+01 angle pdb=" C2' A a1444 " pdb=" C1' A a1444 " pdb=" N9 A a1444 " ideal model delta sigma weight residual 112.00 117.69 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" N ARG R 124 " pdb=" CA ARG R 124 " pdb=" CB ARG R 124 " ideal model delta sigma weight residual 110.28 115.84 -5.56 1.55e+00 4.16e-01 1.29e+01 angle pdb=" N ASN 0 313 " pdb=" CA ASN 0 313 " pdb=" C ASN 0 313 " ideal model delta sigma weight residual 110.31 106.23 4.08 1.20e+00 6.94e-01 1.16e+01 ... (remaining 79723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 30767 35.79 - 71.59: 2597 71.59 - 107.38: 207 107.38 - 143.17: 14 143.17 - 178.96: 12 Dihedral angle restraints: 33597 sinusoidal: 23636 harmonic: 9961 Sorted by residual: dihedral pdb=" O4' U a1416 " pdb=" C1' U a1416 " pdb=" N1 U a1416 " pdb=" C2 U a1416 " ideal model delta sinusoidal sigma weight residual -160.00 0.71 -160.71 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U a1448 " pdb=" C1' U a1448 " pdb=" N1 U a1448 " pdb=" C2 U a1448 " ideal model delta sinusoidal sigma weight residual -160.00 -6.48 -153.52 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U a 369 " pdb=" C1' U a 369 " pdb=" N1 U a 369 " pdb=" C2 U a 369 " ideal model delta sinusoidal sigma weight residual 200.00 46.72 153.28 1 1.50e+01 4.44e-03 8.08e+01 ... (remaining 33594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.218: 9939 4.218 - 8.435: 0 8.435 - 12.653: 0 12.653 - 16.870: 0 16.870 - 21.088: 4 Chirality restraints: 9943 Sorted by residual: chirality pdb="FE3 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.09 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " both_signs ideal model delta sigma weight residual False 10.55 -10.35 20.91 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.31 -20.87 2.00e-01 2.50e+01 1.09e+04 ... (remaining 9940 not shown) Planarity restraints: 5805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 40 " -0.062 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO L 41 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO L 41 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 41 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A a1444 " -0.047 2.00e-02 2.50e+03 2.13e-02 1.25e+01 pdb=" N9 A a1444 " 0.050 2.00e-02 2.50e+03 pdb=" C8 A a1444 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A a1444 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A a1444 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A a1444 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A a1444 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A a1444 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A a1444 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A a1444 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A a1444 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 2 69 " -0.025 2.00e-02 2.50e+03 1.86e-02 8.69e+00 pdb=" CG TRP 2 69 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP 2 69 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP 2 69 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 2 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP 2 69 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 2 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 2 69 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP 2 69 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP 2 69 " -0.000 2.00e-02 2.50e+03 ... (remaining 5802 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 320 2.52 - 3.12: 37275 3.12 - 3.71: 93645 3.71 - 4.31: 131129 4.31 - 4.90: 185226 Nonbonded interactions: 447595 Sorted by model distance: nonbonded pdb=" OP1 C a 356 " pdb="MG MG a1714 " model vdw 1.928 2.170 nonbonded pdb=" OP1 G a 115 " pdb="MG MG a1706 " model vdw 1.946 2.170 nonbonded pdb=" OP2 A a 312 " pdb="MG MG a1727 " model vdw 1.953 2.170 nonbonded pdb=" OP2 A a 110 " pdb="MG MG a1704 " model vdw 1.972 2.170 nonbonded pdb=" OD1 ASP O 65 " pdb=" OH TYR O 251 " model vdw 1.977 2.440 ... (remaining 447590 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 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 16.740 Check model and map are aligned: 0.720 Set scattering table: 0.480 Process input model: 174.240 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54823 Z= 0.216 Angle : 0.660 9.597 79728 Z= 0.353 Chirality : 0.421 21.088 9943 Planarity : 0.005 0.093 5805 Dihedral : 20.916 178.963 27115 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.35 (0.14), residues: 3342 helix: 0.81 (0.12), residues: 1746 sheet: 0.05 (0.31), residues: 288 loop : -0.38 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 2 69 HIS 0.009 0.001 HIS Q 39 PHE 0.025 0.002 PHE E 166 TYR 0.023 0.002 TYR d 523 ARG 0.033 0.001 ARG R 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 503 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 75 LEU cc_start: 0.6853 (mt) cc_final: 0.6547 (pp) REVERT: 5 144 LYS cc_start: 0.7313 (mmmm) cc_final: 0.7040 (mmmt) REVERT: 5 195 ARG cc_start: 0.3948 (mtp-110) cc_final: 0.3602 (mtp-110) REVERT: d 177 MET cc_start: 0.3181 (mpp) cc_final: 0.2259 (ptm) REVERT: d 573 ASN cc_start: 0.6913 (m-40) cc_final: 0.6641 (t0) REVERT: O 56 THR cc_start: 0.6743 (m) cc_final: 0.6361 (p) REVERT: R 108 ARG cc_start: 0.6296 (mmp-170) cc_final: 0.5625 (mmp-170) REVERT: V 126 GLN cc_start: 0.7006 (tt0) cc_final: 0.6798 (tt0) REVERT: 2 35 SER cc_start: 0.7606 (t) cc_final: 0.7403 (t) REVERT: D 4 LYS cc_start: 0.7074 (tttt) cc_final: 0.6631 (tppt) REVERT: E 176 ASN cc_start: 0.7569 (t0) cc_final: 0.7174 (t0) REVERT: F 43 VAL cc_start: 0.8252 (t) cc_final: 0.7777 (t) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.6371 time to fit residues: 531.1960 Evaluate side-chains 372 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 264 optimal weight: 1.9990 chunk 411 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 301 HIS d 567 GLN ** d 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 753 ASN d 778 GLN O 54 GLN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 179 GLN R 133 GLN V 60 HIS ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 92 HIS D 203 ASN D 449 HIS F 78 GLN F 104 GLN 6 46 HIS 6 66 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.238 54823 Z= 0.342 Angle : 0.915 51.168 79728 Z= 0.546 Chirality : 0.129 6.322 9943 Planarity : 0.005 0.066 5805 Dihedral : 21.425 179.217 20883 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.18 % Allowed : 9.07 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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 (0.14), residues: 3342 helix: 1.01 (0.12), residues: 1732 sheet: -0.06 (0.29), residues: 317 loop : -0.32 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP d 761 HIS 0.010 0.001 HIS d 732 PHE 0.023 0.002 PHE O 75 TYR 0.016 0.002 TYR L 123 ARG 0.009 0.001 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 3.830 Fit side-chains revert: symmetry clash REVERT: 5 239 ILE cc_start: 0.5415 (mm) cc_final: 0.5211 (mp) REVERT: d 222 MET cc_start: 0.7335 (mtp) cc_final: 0.7129 (mtp) REVERT: d 621 LYS cc_start: 0.6385 (mmmt) cc_final: 0.5908 (mmtp) REVERT: d 651 SER cc_start: 0.7953 (OUTLIER) cc_final: 0.7447 (p) REVERT: O 56 THR cc_start: 0.6722 (m) cc_final: 0.6354 (p) REVERT: P 54 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6304 (mm-30) REVERT: R 108 ARG cc_start: 0.6732 (mmp-170) cc_final: 0.6077 (mmp-170) REVERT: R 129 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (mp) REVERT: V 134 LYS cc_start: 0.7829 (pptt) cc_final: 0.7618 (mtpt) REVERT: E 176 ASN cc_start: 0.7745 (t0) cc_final: 0.7450 (t0) REVERT: E 205 LEU cc_start: 0.8436 (tp) cc_final: 0.8170 (tt) outliers start: 57 outliers final: 33 residues processed: 417 average time/residue: 0.6058 time to fit residues: 423.4754 Evaluate side-chains 374 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 339 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 262 LEU Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 567 GLN Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 342 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 412 optimal weight: 20.0000 chunk 445 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 408 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 778 GLN ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 83 HIS H 49 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.235 54823 Z= 0.430 Angle : 0.976 50.769 79728 Z= 0.571 Chirality : 0.133 6.392 9943 Planarity : 0.006 0.065 5805 Dihedral : 21.559 179.376 20883 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.25 % Allowed : 13.78 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.05 (0.14), residues: 3342 helix: 0.55 (0.12), residues: 1720 sheet: -0.01 (0.31), residues: 277 loop : -0.69 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 2 69 HIS 0.012 0.002 HIS d 732 PHE 0.026 0.002 PHE 2 44 TYR 0.021 0.002 TYR V 8 ARG 0.009 0.001 ARG Q 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 379 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 237 ARG cc_start: 0.6423 (ptm160) cc_final: 0.5623 (tmm-80) REVERT: d 177 MET cc_start: 0.3550 (mpp) cc_final: 0.2373 (tpt) REVERT: d 183 GLU cc_start: 0.5154 (tt0) cc_final: 0.4835 (pt0) REVERT: d 397 MET cc_start: 0.8445 (mtp) cc_final: 0.7862 (mtp) REVERT: d 450 MET cc_start: 0.7572 (tpp) cc_final: 0.6731 (tpp) REVERT: d 506 MET cc_start: 0.7160 (mmt) cc_final: 0.6465 (mmt) REVERT: d 621 LYS cc_start: 0.6202 (mmmt) cc_final: 0.5658 (mmtm) REVERT: d 651 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7396 (p) REVERT: d 832 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7201 (tm-30) REVERT: P 54 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6109 (mm-30) REVERT: R 108 ARG cc_start: 0.6443 (mmp-170) cc_final: 0.6126 (mmp80) REVERT: R 127 LYS cc_start: 0.8009 (tppt) cc_final: 0.7762 (tppt) REVERT: V 131 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: D 109 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8412 (mp) REVERT: E 176 ASN cc_start: 0.8129 (t0) cc_final: 0.7780 (t0) REVERT: L 100 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7607 (p-80) outliers start: 85 outliers final: 58 residues processed: 430 average time/residue: 0.5961 time to fit residues: 431.0824 Evaluate side-chains 399 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 337 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain 5 residue 318 HIS Chi-restraints excluded: chain d residue 171 VAL Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 262 LEU Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 497 LEU Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 804 ASP Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 131 GLU Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 103 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 413 optimal weight: 30.0000 chunk 437 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN d 289 ASN d 301 HIS d 567 GLN ** d 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS V 192 HIS ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 54823 Z= 0.305 Angle : 0.882 50.626 79728 Z= 0.530 Chirality : 0.131 6.319 9943 Planarity : 0.004 0.057 5805 Dihedral : 21.375 177.976 20883 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.52 % Allowed : 15.58 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.35 (0.14), residues: 3342 helix: 0.94 (0.12), residues: 1722 sheet: -0.13 (0.31), residues: 297 loop : -0.52 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 761 HIS 0.011 0.001 HIS d 732 PHE 0.021 0.002 PHE d 469 TYR 0.026 0.002 TYR d 684 ARG 0.009 0.001 ARG R 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 367 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 237 ARG cc_start: 0.6276 (ptm160) cc_final: 0.5529 (tmm-80) REVERT: d 177 MET cc_start: 0.3514 (mpp) cc_final: 0.2397 (tpt) REVERT: d 183 GLU cc_start: 0.5024 (tt0) cc_final: 0.4786 (pt0) REVERT: d 252 LYS cc_start: 0.6444 (mttt) cc_final: 0.6185 (mtpt) REVERT: d 363 MET cc_start: 0.8128 (mmm) cc_final: 0.7528 (mmt) REVERT: d 397 MET cc_start: 0.8381 (mtp) cc_final: 0.8108 (mtp) REVERT: d 450 MET cc_start: 0.7321 (tpp) cc_final: 0.6247 (tpp) REVERT: d 651 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7412 (p) REVERT: d 832 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7251 (tm-30) REVERT: R 108 ARG cc_start: 0.6341 (mmp-170) cc_final: 0.6034 (mmp80) REVERT: E 162 LYS cc_start: 0.8244 (mttm) cc_final: 0.7711 (mptt) REVERT: E 176 ASN cc_start: 0.7915 (t0) cc_final: 0.7685 (t0) REVERT: E 205 LEU cc_start: 0.8330 (tp) cc_final: 0.8000 (tt) REVERT: E 219 ASP cc_start: 0.8140 (t0) cc_final: 0.7658 (t0) REVERT: H 37 TYR cc_start: 0.8448 (t80) cc_final: 0.8226 (t80) REVERT: L 100 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7583 (p-80) outliers start: 92 outliers final: 58 residues processed: 423 average time/residue: 0.6057 time to fit residues: 429.0321 Evaluate side-chains 398 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 338 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 777 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 112 HIS Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 373 optimal weight: 30.0000 chunk 302 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 175 ASN ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN d 289 ASN d 582 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 54823 Z= 0.364 Angle : 0.920 50.667 79728 Z= 0.545 Chirality : 0.132 6.342 9943 Planarity : 0.005 0.082 5805 Dihedral : 21.362 179.533 20883 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.98 % Allowed : 16.61 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.23 (0.14), residues: 3342 helix: 0.87 (0.12), residues: 1725 sheet: -0.19 (0.31), residues: 296 loop : -0.61 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 761 HIS 0.045 0.002 HIS F 112 PHE 0.017 0.002 PHE 2 44 TYR 0.019 0.002 TYR d 684 ARG 0.022 0.001 ARG F 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 356 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 190 MET cc_start: 0.6119 (tmm) cc_final: 0.5900 (tmm) REVERT: d 177 MET cc_start: 0.3756 (mpp) cc_final: 0.2531 (tpt) REVERT: d 183 GLU cc_start: 0.5190 (tt0) cc_final: 0.4918 (pt0) REVERT: d 252 LYS cc_start: 0.6314 (mttt) cc_final: 0.5955 (mptt) REVERT: d 397 MET cc_start: 0.8378 (mtp) cc_final: 0.8043 (mtp) REVERT: d 450 MET cc_start: 0.7869 (tpp) cc_final: 0.7655 (tpp) REVERT: d 501 MET cc_start: 0.7083 (mmt) cc_final: 0.6800 (mmm) REVERT: d 651 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7381 (p) REVERT: d 684 TYR cc_start: 0.4537 (t80) cc_final: 0.4186 (t80) REVERT: d 832 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7291 (tm-30) REVERT: R 108 ARG cc_start: 0.6190 (mmp-170) cc_final: 0.5941 (mmp-170) REVERT: V 138 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7604 (pp) REVERT: D 109 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (mp) REVERT: E 162 LYS cc_start: 0.8299 (mttm) cc_final: 0.7733 (mptt) REVERT: E 176 ASN cc_start: 0.8022 (t0) cc_final: 0.7724 (t0) REVERT: 6 331 ASP cc_start: 0.7618 (t0) cc_final: 0.7367 (t0) REVERT: H 37 TYR cc_start: 0.8491 (t80) cc_final: 0.8260 (t80) REVERT: H 91 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (tp) REVERT: L 100 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.7745 (p-80) outliers start: 104 outliers final: 73 residues processed: 421 average time/residue: 0.6235 time to fit residues: 441.7890 Evaluate side-chains 415 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 337 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 246 THR Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 631 MET Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain d residue 777 ASP Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 438 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 144 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 54823 Z= 0.299 Angle : 0.875 50.608 79728 Z= 0.526 Chirality : 0.131 6.321 9943 Planarity : 0.004 0.060 5805 Dihedral : 21.284 179.193 20883 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.90 % Allowed : 17.11 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3342 helix: 1.08 (0.12), residues: 1727 sheet: -0.07 (0.31), residues: 289 loop : -0.52 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 761 HIS 0.012 0.001 HIS d 732 PHE 0.016 0.001 PHE O 75 TYR 0.019 0.002 TYR 5 136 ARG 0.006 0.000 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 358 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 163 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8072 (tp) REVERT: 5 190 MET cc_start: 0.6141 (tmm) cc_final: 0.5911 (tmm) REVERT: 5 237 ARG cc_start: 0.5996 (ptm160) cc_final: 0.5324 (tmm-80) REVERT: d 153 ASN cc_start: 0.3536 (OUTLIER) cc_final: 0.3285 (p0) REVERT: d 177 MET cc_start: 0.3970 (mpp) cc_final: 0.2752 (tpt) REVERT: d 183 GLU cc_start: 0.5172 (tt0) cc_final: 0.4929 (pt0) REVERT: d 252 LYS cc_start: 0.6312 (mttt) cc_final: 0.6053 (mptt) REVERT: d 397 MET cc_start: 0.8365 (mtp) cc_final: 0.8002 (mtp) REVERT: d 501 MET cc_start: 0.7238 (mmt) cc_final: 0.6963 (mmm) REVERT: d 651 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7395 (p) REVERT: d 684 TYR cc_start: 0.4441 (t80) cc_final: 0.4191 (t80) REVERT: d 732 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.6126 (m170) REVERT: d 832 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7287 (tm-30) REVERT: O 95 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7994 (mt) REVERT: O 250 ARG cc_start: 0.7143 (mpp-170) cc_final: 0.6805 (mpp-170) REVERT: V 138 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7554 (pp) REVERT: D 109 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8383 (mp) REVERT: E 162 LYS cc_start: 0.8262 (mttm) cc_final: 0.7686 (mptt) REVERT: E 205 LEU cc_start: 0.8349 (tp) cc_final: 0.8028 (tt) REVERT: 6 75 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7865 (mtpt) REVERT: 6 331 ASP cc_start: 0.7614 (t0) cc_final: 0.7322 (t0) REVERT: L 100 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7719 (p-80) outliers start: 102 outliers final: 76 residues processed: 423 average time/residue: 0.6030 time to fit residues: 427.8277 Evaluate side-chains 424 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 339 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 163 LEU Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 246 THR Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 631 MET Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain d residue 732 HIS Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain 6 residue 56 THR Chi-restraints excluded: chain 6 residue 75 LYS Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 194 HIS ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN d 289 ASN d 489 GLN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 752 GLN ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 54823 Z= 0.472 Angle : 1.002 50.709 79728 Z= 0.581 Chirality : 0.133 6.340 9943 Planarity : 0.005 0.059 5805 Dihedral : 21.504 177.064 20883 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 4.98 % Allowed : 16.80 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.20 (0.14), residues: 3342 helix: 0.49 (0.12), residues: 1725 sheet: -0.07 (0.32), residues: 271 loop : -0.87 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 761 HIS 0.056 0.002 HIS d 732 PHE 0.024 0.003 PHE 2 44 TYR 0.019 0.002 TYR d 820 ARG 0.007 0.001 ARG d 731 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 341 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 163 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8075 (tp) REVERT: d 177 MET cc_start: 0.4009 (mpp) cc_final: 0.2968 (tpt) REVERT: d 178 ASP cc_start: 0.4837 (m-30) cc_final: 0.4627 (m-30) REVERT: d 252 LYS cc_start: 0.6352 (mttt) cc_final: 0.5902 (mptt) REVERT: d 501 MET cc_start: 0.7031 (mmt) cc_final: 0.6801 (mmm) REVERT: d 619 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5323 (tt0) REVERT: d 651 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7278 (p) REVERT: V 93 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: V 138 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7569 (pp) REVERT: D 109 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8389 (mp) REVERT: E 162 LYS cc_start: 0.8310 (mttm) cc_final: 0.7694 (mptt) REVERT: 6 75 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7968 (mtpt) REVERT: H 37 TYR cc_start: 0.8517 (t80) cc_final: 0.8315 (t80) outliers start: 130 outliers final: 100 residues processed: 431 average time/residue: 0.6152 time to fit residues: 446.9909 Evaluate side-chains 437 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 330 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 163 LEU Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 225 THR Chi-restraints excluded: chain 5 residue 246 THR Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 171 VAL Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 222 MET Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 430 LEU Chi-restraints excluded: chain d residue 461 LEU Chi-restraints excluded: chain d residue 489 GLN Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 619 GLU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain d residue 777 ASP Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 93 GLN Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain 6 residue 56 THR Chi-restraints excluded: chain 6 residue 75 LYS Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 103 THR Chi-restraints excluded: chain 6 residue 114 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 297 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 343 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN d 289 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 786 GLN V 204 HIS ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 54823 Z= 0.307 Angle : 0.893 50.607 79728 Z= 0.534 Chirality : 0.131 6.318 9943 Planarity : 0.004 0.053 5805 Dihedral : 21.340 178.226 20883 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.75 % Allowed : 18.29 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.22 (0.14), residues: 3342 helix: 0.87 (0.12), residues: 1720 sheet: -0.20 (0.32), residues: 293 loop : -0.64 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 761 HIS 0.048 0.002 HIS 5 194 PHE 0.017 0.002 PHE O 75 TYR 0.023 0.002 TYR d 684 ARG 0.007 0.000 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 356 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 159 MET cc_start: 0.8214 (tpt) cc_final: 0.7840 (tpt) REVERT: 5 163 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7948 (tp) REVERT: 5 210 LYS cc_start: 0.6629 (mmmt) cc_final: 0.5769 (mmtm) REVERT: d 177 MET cc_start: 0.4380 (mpp) cc_final: 0.3248 (tpt) REVERT: d 178 ASP cc_start: 0.4726 (m-30) cc_final: 0.4518 (m-30) REVERT: d 252 LYS cc_start: 0.6141 (mttt) cc_final: 0.5733 (mptt) REVERT: d 450 MET cc_start: 0.8173 (tpp) cc_final: 0.6932 (tpp) REVERT: d 619 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5130 (tt0) REVERT: d 651 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7329 (p) REVERT: V 138 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7555 (pp) REVERT: D 109 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (mp) REVERT: E 153 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7577 (ttm-80) REVERT: E 162 LYS cc_start: 0.8394 (mttm) cc_final: 0.7919 (mptt) REVERT: E 205 LEU cc_start: 0.8322 (tp) cc_final: 0.7989 (tt) REVERT: 6 75 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: H 37 TYR cc_start: 0.8502 (t80) cc_final: 0.8199 (t80) outliers start: 98 outliers final: 78 residues processed: 426 average time/residue: 0.6174 time to fit residues: 438.2054 Evaluate side-chains 421 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 337 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 163 LEU Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 171 VAL Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 246 LYS Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 619 GLU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain d residue 730 LEU Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain 6 residue 75 LYS Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 114 THR Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 244 optimal weight: 30.0000 chunk 177 optimal weight: 7.9990 chunk 319 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 overall best weight: 7.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN ** d 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 GLN ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 54823 Z= 0.434 Angle : 0.974 50.713 79728 Z= 0.569 Chirality : 0.133 6.340 9943 Planarity : 0.005 0.057 5805 Dihedral : 21.385 178.808 20883 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 4.09 % Allowed : 18.52 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.15 (0.14), residues: 3342 helix: 0.57 (0.12), residues: 1712 sheet: -0.13 (0.33), residues: 273 loop : -0.88 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 761 HIS 0.014 0.002 HIS V 204 PHE 0.020 0.002 PHE 2 44 TYR 0.020 0.003 TYR 5 136 ARG 0.009 0.001 ARG d 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 331 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 159 MET cc_start: 0.8234 (tpt) cc_final: 0.7921 (tpt) REVERT: 5 163 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7993 (tp) REVERT: 5 210 LYS cc_start: 0.6692 (mmmt) cc_final: 0.5835 (mmtm) REVERT: d 177 MET cc_start: 0.3996 (mpp) cc_final: 0.2990 (tpt) REVERT: d 252 LYS cc_start: 0.6222 (mttt) cc_final: 0.5765 (mptt) REVERT: d 397 MET cc_start: 0.8529 (mtp) cc_final: 0.8273 (mtp) REVERT: d 619 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5144 (tt0) REVERT: d 651 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7323 (p) REVERT: d 736 MET cc_start: 0.7019 (tpt) cc_final: 0.6717 (tpp) REVERT: V 138 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7604 (pp) REVERT: D 109 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8403 (mp) REVERT: E 162 LYS cc_start: 0.8385 (mttm) cc_final: 0.7846 (mptt) REVERT: 6 75 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7973 (mtpt) REVERT: 6 331 ASP cc_start: 0.7398 (t70) cc_final: 0.7186 (t0) outliers start: 107 outliers final: 87 residues processed: 404 average time/residue: 0.6336 time to fit residues: 429.9782 Evaluate side-chains 413 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 320 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 163 LEU Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 225 THR Chi-restraints excluded: chain 5 residue 230 ILE Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 171 VAL Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 210 GLN Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 430 LEU Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 619 GLU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain O residue 75 PHE Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain 6 residue 56 THR Chi-restraints excluded: chain 6 residue 75 LYS Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 103 THR Chi-restraints excluded: chain 6 residue 114 THR Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.9980 chunk 430 optimal weight: 30.0000 chunk 262 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 451 optimal weight: 10.0000 chunk 415 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 277 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 GLN ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 54823 Z= 0.256 Angle : 0.869 50.661 79728 Z= 0.524 Chirality : 0.131 6.327 9943 Planarity : 0.004 0.050 5805 Dihedral : 21.198 177.016 20883 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.02 % Allowed : 19.82 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.44 (0.15), residues: 3342 helix: 1.07 (0.12), residues: 1724 sheet: -0.09 (0.32), residues: 298 loop : -0.56 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 761 HIS 0.009 0.001 HIS D 139 PHE 0.036 0.001 PHE d 617 TYR 0.022 0.002 TYR d 684 ARG 0.008 0.000 ARG V 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 342 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 159 MET cc_start: 0.8210 (tpt) cc_final: 0.7926 (tpt) REVERT: 5 163 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7901 (tp) REVERT: 5 304 TYR cc_start: 0.5657 (t80) cc_final: 0.5408 (t80) REVERT: d 177 MET cc_start: 0.4317 (mpp) cc_final: 0.3261 (tpt) REVERT: d 252 LYS cc_start: 0.6064 (mttt) cc_final: 0.5734 (mptt) REVERT: d 619 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4738 (tt0) REVERT: d 651 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7283 (p) REVERT: V 138 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7545 (pp) REVERT: D 109 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8349 (mp) REVERT: D 374 PRO cc_start: 0.6224 (Cg_exo) cc_final: 0.6008 (Cg_endo) REVERT: D 382 TYR cc_start: 0.6791 (m-10) cc_final: 0.6546 (m-80) REVERT: E 153 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7628 (ttm-80) REVERT: E 162 LYS cc_start: 0.8363 (mttm) cc_final: 0.7888 (mptt) REVERT: 6 331 ASP cc_start: 0.7301 (t70) cc_final: 0.7078 (t0) outliers start: 79 outliers final: 69 residues processed: 396 average time/residue: 0.6126 time to fit residues: 407.6015 Evaluate side-chains 398 residues out of total 3049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 324 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE Chi-restraints excluded: chain 5 residue 163 LEU Chi-restraints excluded: chain 5 residue 200 ASP Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 225 THR Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 171 VAL Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 222 MET Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 461 LEU Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 619 GLU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain O residue 94 ASN Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 175 GLU Chi-restraints excluded: chain O residue 195 HIS Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain 2 residue 64 ASN Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain 6 residue 91 ASP Chi-restraints excluded: chain 6 residue 114 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 327 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 0.8980 chunk 382 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 369 optimal weight: 10.0000 chunk 45 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 223 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS ** d 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 66 ASN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104955 restraints weight = 166832.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104742 restraints weight = 198610.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105172 restraints weight = 183637.526| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 54823 Z= 0.289 Angle : 0.873 50.578 79728 Z= 0.525 Chirality : 0.131 6.323 9943 Planarity : 0.004 0.051 5805 Dihedral : 21.100 179.749 20883 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.33 % Allowed : 19.67 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.46 (0.15), residues: 3342 helix: 1.06 (0.12), residues: 1742 sheet: -0.03 (0.32), residues: 301 loop : -0.56 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 761 HIS 0.009 0.001 HIS D 139 PHE 0.014 0.001 PHE d 197 TYR 0.022 0.002 TYR 5 136 ARG 0.008 0.000 ARG V 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8673.02 seconds wall clock time: 161 minutes 27.19 seconds (9687.19 seconds total)