Starting phenix.real_space_refine on Sat Dec 28 02:04:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8j_27249/12_2024/8d8j_27249_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8j_27249/12_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/cci-nas-00/data/ceres_data/8d8j_27249/12_2024/8d8j_27249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8j_27249/12_2024/8d8j_27249.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8j_27249/12_2024/8d8j_27249_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8j_27249/12_2024/8d8j_27249_neut.cif" } 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. Time to flip 92 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 21.80, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 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: 9.05 Conformation dependent library (CDL) restraints added in 2.8 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... Secondary structure from input PDB file: 142 helices and 20 sheets defined 56.3% alpha, 10.9% beta 378 base pairs and 638 stacking pairs defined. Time for finding SS restraints: 15.59 Creating SS restraints... Processing helix chain '0' and resid 65 through 72 Processing helix chain '0' and resid 81 through 92 Processing helix chain '0' and resid 97 through 111 removed outlier: 4.022A pdb=" N LEU 0 101 " --> pdb=" O ILE 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 155 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 172 through 183 removed outlier: 3.695A pdb=" N VAL 0 176 " --> pdb=" O ALA 0 172 " (cutoff:3.500A) Processing helix chain '0' and resid 198 through 211 removed outlier: 3.883A pdb=" N GLN 0 202 " --> pdb=" O ASN 0 198 " (cutoff:3.500A) 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 284 through 298 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) Processing helix chain '0' and resid 313 through 329 Processing helix chain '0' and resid 330 through 333 Processing helix chain '0' and resid 385 through 391 removed outlier: 3.581A pdb=" N HIS 0 391 " --> pdb=" O PHE 0 388 " (cutoff:3.500A) Processing helix chain '0' and resid 409 through 416 Processing helix chain '0' and resid 464 through 476 removed outlier: 3.817A pdb=" N ASN 0 476 " --> pdb=" O LEU 0 472 " (cutoff:3.500A) Processing helix chain '0' and resid 490 through 494 removed outlier: 3.687A pdb=" N TRP 0 494 " --> pdb=" O GLN 0 491 " (cutoff:3.500A) Processing helix chain '0' and resid 530 through 538 Processing helix chain '0' and resid 559 through 599 removed outlier: 3.551A pdb=" N LYS 0 563 " --> pdb=" O LEU 0 559 " (cutoff:3.500A) 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 605 through 628 removed outlier: 3.546A pdb=" N ARG 0 627 " --> pdb=" O GLN 0 623 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS 0 628 " --> pdb=" O HIS 0 624 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 57 Processing helix chain '5' and resid 61 through 67 Processing helix chain '5' and resid 70 through 77 removed outlier: 3.517A pdb=" N THR 5 76 " --> pdb=" O GLN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 98 through 104 removed outlier: 4.274A pdb=" N LEU 5 102 " --> pdb=" O SER 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 130 through 137 removed outlier: 3.715A pdb=" N TRP 5 134 " --> pdb=" O LYS 5 130 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE 5 137 " --> pdb=" O ILE 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 152 removed outlier: 3.617A pdb=" N PHE 5 150 " --> pdb=" O LEU 5 146 " (cutoff:3.500A) Processing helix chain '5' and resid 155 through 173 removed outlier: 3.745A pdb=" N MET 5 159 " --> pdb=" O LYS 5 155 " (cutoff:3.500A) 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 175 through 179 removed outlier: 3.833A pdb=" N VAL 5 178 " --> pdb=" O ASN 5 175 " (cutoff:3.500A) Processing helix chain '5' and resid 183 through 199 removed outlier: 3.538A pdb=" N THR 5 187 " --> pdb=" O HIS 5 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 5 199 " --> pdb=" O ARG 5 195 " (cutoff:3.500A) Processing helix chain '5' and resid 203 through 218 removed outlier: 3.770A pdb=" N LYS 5 216 " --> pdb=" O GLN 5 212 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL 5 218 " --> pdb=" O ALA 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 240 Processing helix chain '5' and resid 263 through 288 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 294 through 308 removed outlier: 3.523A pdb=" N GLN 5 298 " --> pdb=" O TYR 5 294 " (cutoff:3.500A) Processing helix chain '5' and resid 313 through 327 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) removed outlier: 3.960A pdb=" N THR 5 327 " --> pdb=" O GLY 5 323 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 153 removed outlier: 3.844A pdb=" N ASN d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 149 through 153' Processing helix chain 'd' and resid 162 through 172 Processing helix chain 'd' and resid 180 through 192 Processing helix chain 'd' and resid 196 through 211 Processing helix chain 'd' and resid 219 through 233 Processing helix chain 'd' and resid 245 through 270 removed outlier: 3.572A pdb=" N LEU d 249 " --> pdb=" O ASP d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 283 through 298 removed outlier: 3.641A pdb=" N LEU d 287 " --> pdb=" O THR d 283 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 315 removed outlier: 3.755A pdb=" N GLY d 315 " --> pdb=" O ARG d 311 " (cutoff:3.500A) Processing helix chain 'd' and resid 319 through 333 Processing helix chain 'd' and resid 335 through 350 removed outlier: 4.382A pdb=" N SER d 350 " --> pdb=" O MET d 346 " (cutoff:3.500A) Processing helix chain 'd' and resid 356 through 371 Processing helix chain 'd' and resid 372 through 386 Processing helix chain 'd' and resid 391 through 406 Processing helix chain 'd' and resid 408 through 413 Processing helix chain 'd' and resid 415 through 433 removed outlier: 3.844A pdb=" N LYS d 433 " --> pdb=" O GLU d 429 " (cutoff:3.500A) Processing helix chain 'd' and resid 440 through 456 removed outlier: 3.698A pdb=" N ASP d 456 " --> pdb=" O LEU d 452 " (cutoff:3.500A) Processing helix chain 'd' and resid 458 through 480 Processing helix chain 'd' and resid 488 through 497 Processing helix chain 'd' and resid 498 through 511 removed outlier: 3.515A pdb=" N LEU d 502 " --> pdb=" O MET d 498 " (cutoff:3.500A) Processing helix chain 'd' and resid 518 through 523 removed outlier: 4.245A pdb=" N GLY d 522 " --> pdb=" O PRO d 518 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR d 523 " --> pdb=" O VAL d 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 518 through 523' Processing helix chain 'd' and resid 523 through 543 Processing helix chain 'd' and resid 564 through 581 Processing helix chain 'd' and resid 582 through 585 removed outlier: 3.602A pdb=" N THR d 585 " --> pdb=" O ASN d 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 582 through 585' Processing helix chain 'd' and resid 592 through 614 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 616 through 636 Processing helix chain 'd' and resid 642 through 657 Proline residue: d 653 - end of helix Processing helix chain 'd' and resid 658 through 669 removed outlier: 3.660A pdb=" N PHE d 662 " --> pdb=" O GLN d 658 " (cutoff:3.500A) Processing helix chain 'd' and resid 672 through 689 Processing helix chain 'd' and resid 719 through 730 Processing helix chain 'd' and resid 731 through 733 No H-bonds generated for 'chain 'd' and resid 731 through 733' Processing helix chain 'd' and resid 737 through 752 Processing helix chain 'd' and resid 753 through 768 Processing helix chain 'd' and resid 770 through 776 removed outlier: 3.687A pdb=" N LEU d 774 " --> pdb=" O THR d 770 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET d 776 " --> pdb=" O PRO d 772 " (cutoff:3.500A) Processing helix chain 'd' and resid 777 through 799 Processing helix chain 'd' and resid 801 through 812 removed outlier: 3.522A pdb=" N SER d 812 " --> pdb=" O ILE d 808 " (cutoff:3.500A) Processing helix chain 'd' and resid 819 through 834 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 835 through 848 Processing helix chain 'O' and resid 35 through 59 removed outlier: 3.805A pdb=" N ALA O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 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 94 through 111 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) removed outlier: 3.967A pdb=" N GLU O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 142 Processing helix chain 'O' and resid 148 through 165 Processing helix chain 'O' and resid 173 through 195 removed outlier: 3.562A pdb=" N HIS O 195 " --> pdb=" O HIS O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 223 Processing helix chain 'O' and resid 223 through 235 Processing helix chain 'O' and resid 237 through 243 removed outlier: 3.640A pdb=" N ILE O 241 " --> pdb=" O ASN O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 256 Processing helix chain 'P' and resid 51 through 58 removed outlier: 3.505A pdb=" N LYS P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 Processing helix chain 'P' and resid 83 through 93 Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'Q' and resid 80 through 117 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) removed outlier: 3.527A pdb=" N LYS Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 135 Processing helix chain 'Q' and resid 171 through 183 Processing helix chain 'R' and resid 88 through 94 removed outlier: 4.460A pdb=" N ALA R 94 " --> pdb=" O GLU R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 101 removed outlier: 3.521A pdb=" N LEU R 99 " --> pdb=" O ARG R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 116 Processing helix chain 'R' and resid 118 through 136 Processing helix chain 'V' and resid 3 through 9 removed outlier: 3.615A pdb=" N GLY V 9 " --> pdb=" O ALA V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 37 removed outlier: 3.741A pdb=" N ILE V 33 " --> pdb=" O GLN V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 78 Processing helix chain 'V' and resid 90 through 149 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) removed outlier: 4.015A pdb=" N SER V 149 " --> pdb=" O LYS V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 155 through 162 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) Processing helix chain 'V' and resid 169 through 206 Processing helix chain 'V' and resid 212 through 223 removed outlier: 3.530A pdb=" N LYS V 218 " --> pdb=" O SER V 214 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 49 Processing helix chain '2' and resid 51 through 54 removed outlier: 3.690A pdb=" N GLU 2 54 " --> pdb=" O ASN 2 51 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 51 through 54' Processing helix chain '2' and resid 55 through 60 Processing helix chain '2' and resid 62 through 67 Processing helix chain '2' and resid 70 through 77 Processing helix chain '2' and resid 80 through 96 Processing helix chain '2' and resid 113 through 127 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 21 through 32 removed outlier: 4.428A pdb=" N GLY D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.622A pdb=" N TYR D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.680A pdb=" N THR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 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 104 through 112 Processing helix chain 'D' and resid 117 through 127 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 167 through 192 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 374 through 380 removed outlier: 3.789A pdb=" N LYS D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 380 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 470 through 484 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 144 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.740A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 254 Processing helix chain 'E' and resid 267 through 281 Processing helix chain 'E' and resid 285 through 293 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'F' and resid 18 through 35 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 109 through 116 Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.525A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 63 Processing helix chain '6' and resid 89 through 94 Processing helix chain '6' and resid 122 through 127 removed outlier: 3.888A pdb=" N GLN 6 126 " --> pdb=" O ASN 6 122 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 135 Processing helix chain '6' and resid 150 through 163 Processing helix chain '6' and resid 167 through 176 Processing helix chain '6' and resid 178 through 199 Processing helix chain '6' and resid 202 through 214 Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'L' and resid 30 through 37 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 142 through 146 Processing sheet with id=AA1, first strand: chain '0' and resid 257 through 260 removed outlier: 5.714A pdb=" N ILE 0 164 " --> pdb=" O ASP 0 192 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL 0 194 " --> pdb=" O ILE 0 164 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP 0 166 " --> pdb=" O VAL 0 194 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG 0 163 " --> pdb=" O TYR 0 269 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR 0 269 " --> pdb=" O ALA 0 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY 0 303 " --> pdb=" O TYR 0 269 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU 0 271 " --> pdb=" O GLY 0 303 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS 0 305 " --> pdb=" O LEU 0 271 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE 0 273 " --> pdb=" O HIS 0 305 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL 0 307 " --> pdb=" O ILE 0 273 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR 0 275 " --> pdb=" O VAL 0 307 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE 0 309 " --> pdb=" O THR 0 275 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY 0 304 " --> pdb=" O ARG 0 458 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 402 through 407 Processing sheet with id=AA3, first strand: chain '0' and resid 496 through 497 Processing sheet with id=AA4, first strand: chain '0' and resid 496 through 497 removed outlier: 3.878A pdb=" N THR 0 551 " --> pdb=" O THR 0 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 670 through 671 Processing sheet with id=AA6, first strand: chain 'P' and resid 81 through 82 removed outlier: 7.136A pdb=" N VAL P 6 " --> pdb=" O GLN P 81 " (cutoff:3.500A) 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) Processing sheet with id=AA7, first strand: chain 'P' and resid 112 through 114 Processing sheet with id=AA8, first strand: chain 'Q' and resid 5 through 13 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) removed outlier: 9.104A pdb=" N LYS Q 70 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE Q 72 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG Q 59 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE Q 77 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU Q 57 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 135 through 136 Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 157 removed outlier: 5.580A pdb=" N MET E 146 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY E 173 " --> pdb=" O MET E 146 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 171 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 163 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 220 through 224 Processing sheet with id=AB3, first strand: chain 'F' and resid 38 through 43 removed outlier: 5.080A pdb=" N VAL F 39 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP F 72 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU F 8 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 47 through 55 removed outlier: 6.669A pdb=" N PHE F 62 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N LYS F 52 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LYS F 60 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU F 2 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 98 through 99 removed outlier: 4.203A pdb=" N LEU 6 98 " --> pdb=" O LEU 6 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 335 through 336 Processing sheet with id=AB7, first strand: chain 'H' and resid 23 through 27 removed outlier: 6.919A pdb=" N ARG H 72 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS H 50 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP H 74 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU H 48 " --> pdb=" O TRP H 74 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY H 76 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 79 through 80 Processing sheet with id=AB9, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AC1, 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=AC2, first strand: chain 'L' and resid 57 through 68 removed outlier: 5.632A pdb=" N VAL L 62 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG L 84 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG L 64 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR L 123 " --> pdb=" O SER L 92 " (cutoff:3.500A) 1456 hydrogen bonds defined for protein. 4230 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: 28.03 Time building geometry restraints manager: 10.88 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: 0.00 - 1.92: 78029 1.92 - 3.84: 1474 3.84 - 5.76: 212 5.76 - 7.68: 11 7.68 - 9.60: 2 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: 318 2.52 - 3.12: 37103 3.12 - 3.71: 93446 3.71 - 4.31: 130669 4.31 - 4.90: 185155 Nonbonded interactions: 446691 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 3.040 ... (remaining 446686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.130 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: 1.470 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 109.330 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.510 ------------------------------------------------------------------------------- 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= 0.219 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 to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 2.831 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: 0.4995 time to fit residues: 417.5148 Evaluate side-chains 372 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 2.842 ------------------------------------------------------------------------------- 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: 2.9990 chunk 117 optimal weight: 6.9990 chunk 231 optimal weight: 0.0670 chunk 183 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 411 optimal weight: 20.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 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 O 54 GLN Q 39 HIS ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 179 GLN R 133 GLN V 55 HIS V 60 HIS ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 92 HIS D 203 ASN D 449 HIS F 104 GLN 6 46 HIS 6 66 ASN 6 83 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.272 54823 Z= 0.368 Angle : 0.912 51.369 79728 Z= 0.545 Chirality : 0.125 5.994 9943 Planarity : 0.005 0.066 5805 Dihedral : 21.447 179.429 20883 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.88 % Allowed : 8.50 % Favored : 89.63 % 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: 0.72 (0.14), residues: 3342 helix: 1.22 (0.12), residues: 1759 sheet: -0.01 (0.29), residues: 308 loop : -0.34 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP d 761 HIS 0.010 0.001 HIS d 732 PHE 0.019 0.002 PHE d 343 TYR 0.016 0.002 TYR L 123 ARG 0.010 0.001 ARG F 40 *********************** 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 449 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 2.892 Fit side-chains revert: symmetry clash REVERT: 5 239 ILE cc_start: 0.5458 (mm) cc_final: 0.5058 (mp) REVERT: d 177 MET cc_start: 0.3095 (mpp) cc_final: 0.2349 (ptm) REVERT: d 573 ASN cc_start: 0.6861 (m-40) cc_final: 0.6560 (m-40) REVERT: d 651 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7390 (p) REVERT: d 729 CYS cc_start: 0.6012 (m) cc_final: 0.5416 (m) REVERT: O 56 THR cc_start: 0.6607 (m) cc_final: 0.6245 (p) REVERT: R 108 ARG cc_start: 0.6728 (mmp-170) cc_final: 0.6166 (mmp80) REVERT: R 129 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8020 (mp) REVERT: E 176 ASN cc_start: 0.7718 (t0) cc_final: 0.7434 (t0) outliers start: 49 outliers final: 27 residues processed: 422 average time/residue: 0.4881 time to fit residues: 346.3370 Evaluate side-chains 369 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 140 ILE 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 412 SER 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 P residue 55 LEU 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 2 residue 109 SER Chi-restraints excluded: chain 2 residue 116 LYS 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 154 VAL Chi-restraints excluded: chain E residue 249 ILE 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 161 ILE 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 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 412 optimal weight: 20.0000 chunk 445 optimal weight: 0.7980 chunk 367 optimal weight: 10.0000 chunk 408 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 194 HIS ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 223 ASN d 301 HIS d 567 GLN d 582 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS H 49 GLN L 124 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 54823 Z= 0.375 Angle : 0.920 50.731 79728 Z= 0.547 Chirality : 0.130 6.276 9943 Planarity : 0.005 0.066 5805 Dihedral : 21.398 177.871 20883 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.49 % Allowed : 12.44 % Favored : 85.07 % 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: 0.56 (0.14), residues: 3342 helix: 1.13 (0.12), residues: 1771 sheet: -0.10 (0.29), residues: 297 loop : -0.48 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 761 HIS 0.009 0.002 HIS d 732 PHE 0.023 0.002 PHE d 617 TYR 0.018 0.002 TYR L 123 ARG 0.013 0.001 ARG F 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 458 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 393 time to evaluate : 2.883 Fit side-chains REVERT: 5 190 MET cc_start: 0.6133 (tmm) cc_final: 0.5931 (ttp) REVERT: d 177 MET cc_start: 0.3377 (mpp) cc_final: 0.2155 (tpt) REVERT: d 359 THR cc_start: 0.8515 (m) cc_final: 0.8295 (p) REVERT: d 397 MET cc_start: 0.8501 (mtp) cc_final: 0.8094 (mtp) REVERT: d 450 MET cc_start: 0.7576 (tpp) cc_final: 0.6618 (tpp) REVERT: d 573 ASN cc_start: 0.7060 (m-40) cc_final: 0.6840 (m-40) REVERT: d 621 LYS cc_start: 0.5873 (mmmt) cc_final: 0.5444 (mmtt) REVERT: d 651 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7332 (p) REVERT: d 684 TYR cc_start: 0.4255 (t80) cc_final: 0.4050 (t80) REVERT: d 832 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7190 (tm-30) REVERT: O 134 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7481 (ttt90) REVERT: R 108 ARG cc_start: 0.6516 (mmp-170) cc_final: 0.6179 (mmp80) REVERT: D 109 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8398 (mp) REVERT: E 176 ASN cc_start: 0.7886 (t0) cc_final: 0.7517 (t0) REVERT: F 107 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6896 (mtp85) REVERT: L 51 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8120 (mm-40) outliers start: 65 outliers final: 43 residues processed: 431 average time/residue: 0.5390 time to fit residues: 390.4507 Evaluate side-chains 394 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 349 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 GLU Chi-restraints excluded: chain 5 residue 107 TYR Chi-restraints excluded: chain 5 residue 140 ILE 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 210 GLN Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 491 THR Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 247 MET Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain Q residue 56 ASP 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 2 residue 79 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 109 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 SER 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 345 ILE 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 68 LEU Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER 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: 5.9990 chunk 213 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 196 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 413 optimal weight: 30.0000 chunk 437 optimal weight: 20.0000 chunk 216 optimal weight: 0.8980 chunk 391 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 196 ASN 5 223 ASN ** d 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 732 HIS ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 192 HIS ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 96 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2140 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= 0.270 Angle : 0.853 50.541 79728 Z= 0.517 Chirality : 0.131 6.359 9943 Planarity : 0.004 0.051 5805 Dihedral : 21.225 178.408 20883 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.22 % Allowed : 14.20 % Favored : 83.58 % 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: 1.06 (0.14), residues: 3342 helix: 1.56 (0.12), residues: 1783 sheet: 0.10 (0.29), residues: 302 loop : -0.32 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 761 HIS 0.007 0.001 HIS d 732 PHE 0.023 0.001 PHE d 469 TYR 0.015 0.001 TYR 5 315 ARG 0.008 0.000 ARG 6 332 *********************** 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 443 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 385 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: 5 237 ARG cc_start: 0.6293 (ptm160) cc_final: 0.5635 (tmm-80) REVERT: 5 283 THR cc_start: 0.6671 (p) cc_final: 0.6414 (t) REVERT: d 177 MET cc_start: 0.3366 (mpp) cc_final: 0.2176 (tpt) REVERT: d 397 MET cc_start: 0.8364 (mtp) cc_final: 0.7723 (mtp) REVERT: d 573 ASN cc_start: 0.7150 (m-40) cc_final: 0.6789 (m-40) REVERT: d 632 GLN cc_start: 0.7030 (mt0) cc_final: 0.6712 (tt0) REVERT: d 651 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7311 (p) REVERT: d 684 TYR cc_start: 0.4202 (t80) cc_final: 0.3926 (t80) REVERT: d 832 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7194 (tm-30) REVERT: P 55 LEU cc_start: 0.7141 (mt) cc_final: 0.6853 (tt) REVERT: R 108 ARG cc_start: 0.6329 (mmp-170) cc_final: 0.6072 (mmp80) REVERT: V 209 PHE cc_start: 0.6339 (m-80) cc_final: 0.5677 (m-80) REVERT: V 210 ILE cc_start: 0.8669 (mt) cc_final: 0.8457 (mt) REVERT: E 176 ASN cc_start: 0.7684 (t0) cc_final: 0.7432 (t0) REVERT: E 219 ASP cc_start: 0.8022 (t0) cc_final: 0.7644 (t0) REVERT: E 277 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6835 (mt-10) REVERT: F 107 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6889 (mtp85) REVERT: 6 51 ASP cc_start: 0.8535 (t0) cc_final: 0.8334 (t0) REVERT: H 37 TYR cc_start: 0.8422 (t80) cc_final: 0.8209 (t80) REVERT: L 51 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8090 (mm-40) outliers start: 58 outliers final: 36 residues processed: 418 average time/residue: 0.4944 time to fit residues: 345.5529 Evaluate side-chains 380 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 253 ILE Chi-restraints excluded: chain 5 residue 318 HIS Chi-restraints excluded: chain d residue 412 SER 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 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 119 THR Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 155 THR Chi-restraints excluded: chain V residue 162 GLN 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 443 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 45 MET 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 345 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER 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: 0.6980 chunk 6 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 180 optimal weight: 0.0170 chunk 373 optimal weight: 30.0000 chunk 302 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 overall best weight: 3.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 659 GLN d 732 HIS d 753 ASN O 187 ASN ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 215 GLN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2431 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= 0.315 Angle : 0.873 50.652 79728 Z= 0.526 Chirality : 0.131 6.338 9943 Planarity : 0.004 0.054 5805 Dihedral : 21.133 177.961 20883 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.25 % Allowed : 14.58 % Favored : 82.17 % 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: 1.00 (0.14), residues: 3342 helix: 1.53 (0.12), residues: 1776 sheet: 0.08 (0.30), residues: 295 loop : -0.36 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 761 HIS 0.009 0.001 HIS d 732 PHE 0.014 0.002 PHE d 343 TYR 0.018 0.002 TYR 5 315 ARG 0.012 0.001 ARG R 130 *********************** 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 458 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 373 time to evaluate : 2.904 Fit side-chains revert: symmetry clash REVERT: d 177 MET cc_start: 0.3312 (mpp) cc_final: 0.2219 (tpt) REVERT: d 397 MET cc_start: 0.8404 (mtp) cc_final: 0.7889 (mtp) REVERT: d 450 MET cc_start: 0.7485 (tpp) cc_final: 0.6496 (tpp) REVERT: d 651 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7316 (p) REVERT: d 684 TYR cc_start: 0.4227 (t80) cc_final: 0.3923 (t80) REVERT: d 832 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7258 (tm-30) REVERT: O 196 ARG cc_start: 0.6911 (ptp-170) cc_final: 0.6553 (ptp-170) REVERT: P 55 LEU cc_start: 0.7027 (mt) cc_final: 0.6759 (tt) REVERT: R 108 ARG cc_start: 0.6179 (mmp-170) cc_final: 0.5906 (mmp-170) REVERT: V 209 PHE cc_start: 0.6534 (m-80) cc_final: 0.6100 (m-80) REVERT: 2 54 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7033 (mp0) REVERT: D 109 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8337 (mp) REVERT: E 176 ASN cc_start: 0.7792 (t0) cc_final: 0.7485 (t0) REVERT: F 107 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.7018 (mtp85) REVERT: 6 58 MET cc_start: 0.7957 (tpt) cc_final: 0.7571 (tpt) REVERT: H 104 GLU cc_start: 0.7709 (pm20) cc_final: 0.7505 (pm20) REVERT: L 51 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8055 (mm-40) outliers start: 85 outliers final: 64 residues processed: 423 average time/residue: 0.5567 time to fit residues: 398.1165 Evaluate side-chains 401 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 335 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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 140 ILE 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 171 VAL 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 497 LEU Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 638 VAL Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 722 HIS 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 29 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 127 LYS Chi-restraints excluded: chain V residue 155 THR Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 79 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 109 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 196 VAL 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 154 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 112 HIS 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 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE 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 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER 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: 9.9990 chunk 257 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 438 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 144 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 573 ASN d 732 HIS ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 215 GLN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 54823 Z= 0.364 Angle : 0.904 50.665 79728 Z= 0.539 Chirality : 0.131 6.348 9943 Planarity : 0.004 0.078 5805 Dihedral : 21.164 178.732 20883 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.64 % Allowed : 15.38 % Favored : 80.98 % 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: 0.74 (0.14), residues: 3342 helix: 1.31 (0.12), residues: 1778 sheet: 0.04 (0.29), residues: 306 loop : -0.49 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 761 HIS 0.047 0.002 HIS F 112 PHE 0.021 0.002 PHE d 469 TYR 0.028 0.002 TYR 5 136 ARG 0.013 0.001 ARG F 113 *********************** 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 457 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 362 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: 5 190 MET cc_start: 0.6295 (tmm) cc_final: 0.6016 (tmm) REVERT: d 177 MET cc_start: 0.3605 (mpp) cc_final: 0.2543 (tpt) REVERT: d 450 MET cc_start: 0.7761 (tpp) cc_final: 0.6676 (tpp) REVERT: d 493 TRP cc_start: 0.7505 (m100) cc_final: 0.7195 (m100) REVERT: d 619 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4785 (tt0) REVERT: d 651 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7313 (p) REVERT: d 832 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7333 (tm-30) REVERT: O 196 ARG cc_start: 0.6978 (ptp-170) cc_final: 0.6522 (ptp-170) REVERT: P 55 LEU cc_start: 0.7036 (mt) cc_final: 0.6742 (tt) REVERT: R 108 ARG cc_start: 0.6087 (mmp-170) cc_final: 0.5749 (mmp80) REVERT: V 138 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7636 (pp) REVERT: D 3 ARG cc_start: 0.6594 (mmt90) cc_final: 0.6343 (mtp85) REVERT: D 58 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 109 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8344 (mp) REVERT: E 176 ASN cc_start: 0.7809 (t0) cc_final: 0.7553 (t0) REVERT: 6 331 ASP cc_start: 0.7540 (t0) cc_final: 0.7269 (t0) REVERT: H 37 TYR cc_start: 0.8409 (t80) cc_final: 0.8149 (t80) REVERT: L 51 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8055 (mm-40) outliers start: 95 outliers final: 67 residues processed: 420 average time/residue: 0.5032 time to fit residues: 354.4595 Evaluate side-chains 414 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 343 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 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 171 VAL 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 497 LEU 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 128 ILE 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 119 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain R residue 103 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 155 THR Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 79 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 109 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 95 SER 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 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE 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 61 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER 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: 0.9990 chunk 320 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 368 optimal weight: 10.0000 chunk 244 optimal weight: 30.0000 chunk 436 optimal weight: 20.0000 chunk 273 optimal weight: 0.0170 chunk 266 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 573 ASN d 732 HIS ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2892 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= 0.283 Angle : 0.858 50.613 79728 Z= 0.519 Chirality : 0.130 6.333 9943 Planarity : 0.004 0.050 5805 Dihedral : 21.075 179.596 20883 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.83 % Allowed : 16.42 % Favored : 80.75 % 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: 1.02 (0.14), residues: 3342 helix: 1.55 (0.12), residues: 1782 sheet: 0.09 (0.30), residues: 307 loop : -0.36 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 761 HIS 0.011 0.001 HIS d 732 PHE 0.020 0.001 PHE d 469 TYR 0.016 0.001 TYR 5 136 ARG 0.008 0.000 ARG V 128 *********************** 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 428 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 354 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: 5 190 MET cc_start: 0.6261 (tmm) cc_final: 0.6023 (tmm) REVERT: 5 237 ARG cc_start: 0.6153 (ptm160) cc_final: 0.5522 (tmm-80) REVERT: d 177 MET cc_start: 0.3557 (mpp) cc_final: 0.2545 (tpt) REVERT: d 450 MET cc_start: 0.7776 (tpp) cc_final: 0.6650 (tpp) REVERT: d 619 GLU cc_start: 0.5010 (OUTLIER) cc_final: 0.4293 (tt0) REVERT: d 651 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7294 (p) REVERT: d 832 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7348 (tm-30) REVERT: O 144 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: O 196 ARG cc_start: 0.6934 (ptp-170) cc_final: 0.6571 (ptp-170) REVERT: P 55 LEU cc_start: 0.7029 (mt) cc_final: 0.6748 (tt) REVERT: R 108 ARG cc_start: 0.6021 (mmp-170) cc_final: 0.5784 (mmp-170) REVERT: V 138 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7591 (pp) REVERT: D 3 ARG cc_start: 0.6630 (mmt90) cc_final: 0.6400 (mtp85) REVERT: D 58 GLU cc_start: 0.7242 (tm-30) cc_final: 0.7009 (tm-30) REVERT: D 109 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8325 (mp) REVERT: E 219 ASP cc_start: 0.8266 (t0) cc_final: 0.7919 (t0) REVERT: 6 51 ASP cc_start: 0.8434 (t0) cc_final: 0.8230 (t0) REVERT: 6 58 MET cc_start: 0.7972 (tpt) cc_final: 0.7582 (tpt) REVERT: H 37 TYR cc_start: 0.8439 (t80) cc_final: 0.8189 (t80) REVERT: H 104 GLU cc_start: 0.7867 (pm20) cc_final: 0.7528 (pm20) REVERT: L 51 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8059 (mm-40) outliers start: 74 outliers final: 56 residues processed: 395 average time/residue: 0.5060 time to fit residues: 332.2091 Evaluate side-chains 394 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 2.874 ------------------------------------------------------------------------------- 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 218 VAL 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 218 PHE Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 497 LEU 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 128 ILE Chi-restraints excluded: chain O residue 144 MET 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 85 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 182 LEU 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 V residue 155 THR Chi-restraints excluded: chain V residue 162 GLN 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 196 VAL 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 154 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 84 optimal weight: 0.0010 chunk 277 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 343 optimal weight: 20.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 573 ASN ** d 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 54823 Z= 0.410 Angle : 0.937 50.611 79728 Z= 0.553 Chirality : 0.132 6.343 9943 Planarity : 0.005 0.056 5805 Dihedral : 21.192 176.720 20883 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.21 % Allowed : 16.92 % Favored : 79.87 % 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: 0.55 (0.14), residues: 3342 helix: 1.15 (0.12), residues: 1781 sheet: -0.07 (0.30), residues: 306 loop : -0.57 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 2 69 HIS 0.013 0.002 HIS d 732 PHE 0.025 0.002 PHE d 620 TYR 0.017 0.002 TYR d 820 ARG 0.009 0.001 ARG H 98 *********************** 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 431 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 3.165 Fit side-chains REVERT: 5 190 MET cc_start: 0.6361 (tmm) cc_final: 0.6030 (tmm) REVERT: d 177 MET cc_start: 0.4026 (mpp) cc_final: 0.2812 (tpt) REVERT: d 396 ILE cc_start: 0.8975 (mt) cc_final: 0.8392 (pt) REVERT: d 619 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4423 (tt0) REVERT: d 651 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7294 (p) REVERT: d 832 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7394 (tm-30) REVERT: O 134 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7778 (ttt90) REVERT: P 29 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6903 (ttp-170) REVERT: R 108 ARG cc_start: 0.6069 (mmp-170) cc_final: 0.5617 (mmp80) REVERT: V 134 LYS cc_start: 0.8012 (pptt) cc_final: 0.7759 (mtmt) REVERT: V 138 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7623 (pp) REVERT: D 3 ARG cc_start: 0.6624 (mmt90) cc_final: 0.6371 (mtp85) REVERT: D 58 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7132 (tm-30) REVERT: D 109 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (mp) REVERT: E 176 ASN cc_start: 0.7811 (t0) cc_final: 0.7472 (t0) REVERT: 6 331 ASP cc_start: 0.7562 (t0) cc_final: 0.7332 (t70) REVERT: H 37 TYR cc_start: 0.8498 (t80) cc_final: 0.8270 (t80) REVERT: H 104 GLU cc_start: 0.7991 (pm20) cc_final: 0.7739 (pm20) REVERT: L 51 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8020 (mm-40) REVERT: L 66 MET cc_start: 0.8185 (ptm) cc_final: 0.7913 (ptp) outliers start: 84 outliers final: 67 residues processed: 402 average time/residue: 0.4879 time to fit residues: 329.0900 Evaluate side-chains 410 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 338 time to evaluate : 2.830 ------------------------------------------------------------------------------- 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 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 210 GLN Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 358 CYS Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 497 LEU Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 571 GLU Chi-restraints excluded: chain d residue 619 GLU 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 O residue 128 ILE Chi-restraints excluded: chain O residue 133 ASP 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 119 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 182 LEU 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 V residue 155 THR Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain 2 residue 79 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 109 LEU Chi-restraints excluded: chain D residue 196 VAL 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 142 ARG Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN 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 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 126 LEU 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 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER 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: 9.9990 chunk 177 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 367 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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** d 573 ASN ** d 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 62 ASN 2 65 ASN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 54823 Z= 0.410 Angle : 0.952 50.715 79728 Z= 0.560 Chirality : 0.132 6.343 9943 Planarity : 0.005 0.056 5805 Dihedral : 21.333 179.575 20883 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.44 % Allowed : 17.34 % Favored : 79.22 % 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: 0.19 (0.14), residues: 3342 helix: 0.86 (0.12), residues: 1778 sheet: -0.12 (0.31), residues: 287 loop : -0.76 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 761 HIS 0.013 0.002 HIS d 732 PHE 0.026 0.002 PHE d 380 TYR 0.018 0.002 TYR F 49 ARG 0.010 0.001 ARG H 98 *********************** 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 440 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 350 time to evaluate : 2.927 Fit side-chains REVERT: 5 237 ARG cc_start: 0.6366 (ptm160) cc_final: 0.5619 (tmm-80) REVERT: d 177 MET cc_start: 0.4597 (mpp) cc_final: 0.3279 (tpt) REVERT: d 314 TYR cc_start: 0.6526 (m-10) cc_final: 0.6317 (m-10) REVERT: d 619 GLU cc_start: 0.5138 (OUTLIER) cc_final: 0.4457 (tt0) REVERT: d 651 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7323 (p) REVERT: d 832 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7578 (tm-30) REVERT: O 134 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7773 (ttt90) REVERT: P 29 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6875 (ttp-170) REVERT: R 108 ARG cc_start: 0.6255 (mmp-170) cc_final: 0.5845 (mmp-170) REVERT: V 138 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7583 (pp) REVERT: D 3 ARG cc_start: 0.6507 (mmt90) cc_final: 0.6300 (mtp85) REVERT: D 58 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 109 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (mp) REVERT: E 176 ASN cc_start: 0.7873 (t0) cc_final: 0.7648 (t0) REVERT: H 37 TYR cc_start: 0.8526 (t80) cc_final: 0.8289 (t80) REVERT: H 104 GLU cc_start: 0.7918 (pm20) cc_final: 0.7653 (pm20) REVERT: L 51 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8069 (mm-40) REVERT: L 66 MET cc_start: 0.8151 (ptm) cc_final: 0.7931 (ptp) REVERT: L 116 GLN cc_start: 0.7358 (mp10) cc_final: 0.7118 (mp10) outliers start: 90 outliers final: 65 residues processed: 410 average time/residue: 0.5101 time to fit residues: 345.8248 Evaluate side-chains 399 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 2.842 ------------------------------------------------------------------------------- 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 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 210 GLN Chi-restraints excluded: chain d residue 218 PHE Chi-restraints excluded: chain d residue 358 CYS Chi-restraints excluded: chain d residue 412 SER Chi-restraints excluded: chain d residue 497 LEU Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 571 GLU 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 128 ILE 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 119 THR Chi-restraints excluded: chain Q residue 96 VAL 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 V residue 155 THR 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 196 VAL 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 142 ARG 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 268 ASP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN 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 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain 6 residue 345 ILE 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 61 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.8980 chunk 430 optimal weight: 30.0000 chunk 262 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 299 optimal weight: 0.8980 chunk 451 optimal weight: 3.9990 chunk 415 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 277 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 573 ASN d 732 HIS V 204 HIS 2 62 ASN 2 65 ASN E 225 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 54823 Z= 0.296 Angle : 0.879 50.647 79728 Z= 0.528 Chirality : 0.131 6.324 9943 Planarity : 0.004 0.052 5805 Dihedral : 21.148 179.583 20883 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 17.99 % Favored : 79.33 % 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: 0.69 (0.14), residues: 3342 helix: 1.25 (0.12), residues: 1795 sheet: -0.03 (0.30), residues: 309 loop : -0.50 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 761 HIS 0.011 0.001 HIS d 732 PHE 0.016 0.001 PHE d 469 TYR 0.019 0.001 TYR 5 136 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 424 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 3.098 Fit side-chains REVERT: 5 197 ARG cc_start: 0.5232 (tmt-80) cc_final: 0.5026 (tmt170) REVERT: 5 237 ARG cc_start: 0.6281 (ptm160) cc_final: 0.5695 (tmm-80) REVERT: d 177 MET cc_start: 0.4271 (mpp) cc_final: 0.3110 (tpt) REVERT: d 224 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7261 (tt0) REVERT: d 397 MET cc_start: 0.8386 (mtp) cc_final: 0.8165 (mtp) REVERT: d 619 GLU cc_start: 0.5141 (OUTLIER) cc_final: 0.4400 (tt0) REVERT: d 651 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7310 (p) REVERT: d 732 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.4403 (m-70) REVERT: d 832 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7580 (tm-30) REVERT: O 134 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7805 (ttt90) REVERT: V 138 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7637 (pp) REVERT: D 3 ARG cc_start: 0.6627 (mmt90) cc_final: 0.6410 (mtp85) REVERT: D 58 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 109 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8332 (mp) REVERT: E 153 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7608 (ttm-80) REVERT: E 176 ASN cc_start: 0.7621 (t0) cc_final: 0.7300 (t0) REVERT: 6 58 MET cc_start: 0.7951 (tpt) cc_final: 0.7534 (tpt) REVERT: H 104 GLU cc_start: 0.7958 (pm20) cc_final: 0.7733 (pm20) REVERT: L 51 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8019 (mm-40) REVERT: L 66 MET cc_start: 0.8191 (ptm) cc_final: 0.7949 (ptp) outliers start: 70 outliers final: 62 residues processed: 399 average time/residue: 0.5159 time to fit residues: 338.1236 Evaluate side-chains 396 residues out of total 3049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 329 time to evaluate : 2.858 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain 5 residue 201 TYR Chi-restraints excluded: chain 5 residue 218 VAL Chi-restraints excluded: chain 5 residue 277 ILE Chi-restraints excluded: chain d residue 171 VAL 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 497 LEU Chi-restraints excluded: chain d residue 569 LEU Chi-restraints excluded: chain d residue 571 GLU Chi-restraints excluded: chain d residue 619 GLU Chi-restraints excluded: chain d residue 651 SER Chi-restraints excluded: chain d residue 670 THR Chi-restraints excluded: chain d residue 722 HIS Chi-restraints excluded: chain d residue 732 HIS Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 144 MET 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 85 THR 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 78 THR 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 155 THR Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain V residue 204 HIS 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 196 VAL 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 142 ARG Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain 6 residue 103 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 161 ILE Chi-restraints excluded: chain 6 residue 194 SER Chi-restraints excluded: chain 6 residue 345 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 0.9990 chunk 382 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 45 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 89 GLN d 573 ASN d 732 HIS ** O 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 HIS 2 62 ASN 2 64 ASN 2 65 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104504 restraints weight = 166476.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104280 restraints weight = 199910.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104779 restraints weight = 179286.230| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 54823 Z= 0.390 Angle : 0.932 50.713 79728 Z= 0.551 Chirality : 0.132 6.354 9943 Planarity : 0.005 0.055 5805 Dihedral : 21.154 179.589 20883 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.02 % Allowed : 17.87 % Favored : 79.10 % 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: 1784 sheet: -0.06 (0.30), residues: 310 loop : -0.60 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 761 HIS 0.019 0.002 HIS d 732 PHE 0.030 0.002 PHE V 209 TYR 0.022 0.002 TYR V 203 ARG 0.009 0.001 ARG V 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6954.68 seconds wall clock time: 125 minutes 25.51 seconds (7525.51 seconds total)