Starting phenix.real_space_refine on Mon Mar 18 23:09:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn6_29306/03_2024/8fn6_29306_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 124 5.16 5 C 13997 2.51 5 N 3921 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 194": "OE1" <-> "OE2" Residue "1 ASP 308": "OD1" <-> "OD2" Residue "1 ASP 396": "OD1" <-> "OD2" Residue "1 TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 98": "OE1" <-> "OE2" Residue "2 GLU 226": "OE1" <-> "OE2" Residue "2 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 46": "OE1" <-> "OE2" Residue "3 TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 654": "OE1" <-> "OE2" Residue "4 ASP 691": "OD1" <-> "OD2" Residue "4 TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 1077": "OE1" <-> "OE2" Residue "5 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 145": "OD1" <-> "OD2" Residue "6 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 442": "OD1" <-> "OD2" Residue "6 GLU 487": "OE1" <-> "OE2" Residue "6 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22421 Number of models: 1 Model: "" Number of chains: 8 Chain: "g" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 960 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 22} Link IDs: {'rna2p': 5, 'rna3p': 40} Chain breaks: 1 Chain: "1" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain: "2" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3421 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3705 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain: "4" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5790 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain breaks: 1 Chain: "5" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2163 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain: "6" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3583 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 11, 'TRANS': 440} Chain: "g" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.24, per 1000 atoms: 0.55 Number of scatterers: 22421 At special positions: 0 Unit cell: (115.5, 139.7, 213.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 49 15.00 O 4330 8.00 N 3921 7.00 C 13997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 4.1 seconds 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 13 sheets defined 51.9% alpha, 7.3% beta 18 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 9.24 Creating SS restraints... Processing helix chain '1' and resid 196 through 216 Processing helix chain '1' and resid 246 through 254 removed outlier: 4.030A pdb=" N GLN 1 254 " --> pdb=" O GLN 1 250 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 273 No H-bonds generated for 'chain '1' and resid 270 through 273' Processing helix chain '1' and resid 278 through 281 No H-bonds generated for 'chain '1' and resid 278 through 281' Processing helix chain '1' and resid 350 through 358 removed outlier: 4.122A pdb=" N ALA 1 357 " --> pdb=" O VAL 1 353 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER 1 358 " --> pdb=" O GLU 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 441 through 460 removed outlier: 3.553A pdb=" N GLY 1 445 " --> pdb=" O VAL 1 441 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG 1 454 " --> pdb=" O GLU 1 450 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 1 455 " --> pdb=" O LEU 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 462 through 465 No H-bonds generated for 'chain '1' and resid 462 through 465' Processing helix chain '2' and resid 51 through 59 Processing helix chain '2' and resid 68 through 77 Processing helix chain '2' and resid 90 through 103 Processing helix chain '2' and resid 134 through 137 No H-bonds generated for 'chain '2' and resid 134 through 137' Processing helix chain '2' and resid 193 through 195 No H-bonds generated for 'chain '2' and resid 193 through 195' Processing helix chain '2' and resid 213 through 235 removed outlier: 3.588A pdb=" N TRP 2 227 " --> pdb=" O MET 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 254 No H-bonds generated for 'chain '2' and resid 252 through 254' Processing helix chain '2' and resid 256 through 258 No H-bonds generated for 'chain '2' and resid 256 through 258' Processing helix chain '2' and resid 264 through 274 Processing helix chain '2' and resid 287 through 298 Processing helix chain '2' and resid 366 through 372 Processing helix chain '2' and resid 450 through 452 No H-bonds generated for 'chain '2' and resid 450 through 452' Processing helix chain '2' and resid 457 through 473 Processing helix chain '3' and resid 4 through 18 Processing helix chain '3' and resid 25 through 35 Processing helix chain '3' and resid 39 through 61 removed outlier: 4.394A pdb=" N LEU 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN 3 55 " --> pdb=" O LEU 3 51 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN 3 56 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG 3 57 " --> pdb=" O ALA 3 53 " (cutoff:3.500A) Processing helix chain '3' and resid 89 through 100 Processing helix chain '3' and resid 107 through 118 Processing helix chain '3' and resid 125 through 133 Processing helix chain '3' and resid 143 through 160 Proline residue: 3 152 - end of helix removed outlier: 3.703A pdb=" N ARG 3 155 " --> pdb=" O LEU 3 151 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 3 156 " --> pdb=" O PRO 3 152 " (cutoff:3.500A) Proline residue: 3 159 - end of helix Processing helix chain '3' and resid 163 through 175 removed outlier: 4.404A pdb=" N HIS 3 168 " --> pdb=" O ARG 3 164 " (cutoff:3.500A) Processing helix chain '3' and resid 184 through 193 Processing helix chain '3' and resid 200 through 209 Processing helix chain '3' and resid 215 through 224 Processing helix chain '3' and resid 226 through 235 Processing helix chain '3' and resid 239 through 256 Processing helix chain '3' and resid 261 through 273 Processing helix chain '3' and resid 280 through 290 removed outlier: 3.668A pdb=" N PHE 3 290 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 298 through 308 Processing helix chain '3' and resid 313 through 315 No H-bonds generated for 'chain '3' and resid 313 through 315' Processing helix chain '3' and resid 322 through 334 Processing helix chain '3' and resid 341 through 354 removed outlier: 4.402A pdb=" N ASN 3 353 " --> pdb=" O ASN 3 349 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 371 Processing helix chain '3' and resid 375 through 384 Proline residue: 3 379 - end of helix Processing helix chain '3' and resid 388 through 395 removed outlier: 3.965A pdb=" N HIS 3 395 " --> pdb=" O ARG 3 391 " (cutoff:3.500A) Processing helix chain '3' and resid 400 through 412 Processing helix chain '3' and resid 419 through 434 Proline residue: 3 427 - end of helix Processing helix chain '3' and resid 441 through 456 Processing helix chain '3' and resid 463 through 480 Processing helix chain '4' and resid 337 through 345 Processing helix chain '4' and resid 352 through 359 removed outlier: 3.986A pdb=" N PHE 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 368 through 380 removed outlier: 4.051A pdb=" N GLU 4 380 " --> pdb=" O CYS 4 376 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 394 Processing helix chain '4' and resid 401 through 413 Processing helix chain '4' and resid 440 through 451 Processing helix chain '4' and resid 468 through 487 removed outlier: 4.067A pdb=" N GLY 4 487 " --> pdb=" O SER 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 491 through 502 Processing helix chain '4' and resid 509 through 521 Processing helix chain '4' and resid 526 through 539 Processing helix chain '4' and resid 544 through 564 Proline residue: 4 552 - end of helix Processing helix chain '4' and resid 573 through 589 removed outlier: 3.814A pdb=" N GLU 4 588 " --> pdb=" O THR 4 584 " (cutoff:3.500A) Processing helix chain '4' and resid 596 through 608 removed outlier: 3.616A pdb=" N LYS 4 607 " --> pdb=" O HIS 4 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN 4 608 " --> pdb=" O THR 4 604 " (cutoff:3.500A) Processing helix chain '4' and resid 614 through 628 Proline residue: 4 618 - end of helix removed outlier: 3.648A pdb=" N ARG 4 626 " --> pdb=" O LEU 4 622 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR 4 627 " --> pdb=" O LEU 4 623 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG 4 628 " --> pdb=" O CYS 4 624 " (cutoff:3.500A) Processing helix chain '4' and resid 630 through 632 No H-bonds generated for 'chain '4' and resid 630 through 632' Processing helix chain '4' and resid 644 through 646 No H-bonds generated for 'chain '4' and resid 644 through 646' Processing helix chain '4' and resid 649 through 659 removed outlier: 3.852A pdb=" N GLY 4 653 " --> pdb=" O ASP 4 649 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU 4 654 " --> pdb=" O ASP 4 650 " (cutoff:3.500A) Processing helix chain '4' and resid 663 through 665 No H-bonds generated for 'chain '4' and resid 663 through 665' Processing helix chain '4' and resid 668 through 683 Processing helix chain '4' and resid 690 through 706 removed outlier: 3.673A pdb=" N GLN 4 703 " --> pdb=" O VAL 4 699 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY 4 704 " --> pdb=" O TRP 4 700 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP 4 705 " --> pdb=" O LEU 4 701 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS 4 706 " --> pdb=" O ARG 4 702 " (cutoff:3.500A) Processing helix chain '4' and resid 712 through 719 Processing helix chain '4' and resid 722 through 724 No H-bonds generated for 'chain '4' and resid 722 through 724' Processing helix chain '4' and resid 727 through 736 Processing helix chain '4' and resid 745 through 750 Processing helix chain '4' and resid 755 through 760 removed outlier: 3.890A pdb=" N LEU 4 758 " --> pdb=" O PRO 4 755 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU 4 759 " --> pdb=" O ARG 4 756 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 4 760 " --> pdb=" O ARG 4 757 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 755 through 760' Processing helix chain '4' and resid 763 through 774 Processing helix chain '4' and resid 776 through 780 Processing helix chain '4' and resid 783 through 798 removed outlier: 4.539A pdb=" N LEU 4 787 " --> pdb=" O SER 4 784 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL 4 788 " --> pdb=" O HIS 4 785 " (cutoff:3.500A) Processing helix chain '4' and resid 806 through 819 removed outlier: 3.921A pdb=" N MET 4 819 " --> pdb=" O GLY 4 815 " (cutoff:3.500A) Processing helix chain '4' and resid 825 through 832 removed outlier: 3.567A pdb=" N THR 4 832 " --> pdb=" O ASN 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 849 through 856 Processing helix chain '4' and resid 863 through 875 Processing helix chain '4' and resid 885 through 893 removed outlier: 3.746A pdb=" N ARG 4 890 " --> pdb=" O LEU 4 886 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 4 891 " --> pdb=" O LEU 4 887 " (cutoff:3.500A) Processing helix chain '4' and resid 900 through 912 Processing helix chain '4' and resid 919 through 932 removed outlier: 3.599A pdb=" N PHE 4 929 " --> pdb=" O LEU 4 925 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU 4 932 " --> pdb=" O SER 4 928 " (cutoff:3.500A) Processing helix chain '4' and resid 937 through 949 removed outlier: 4.047A pdb=" N SER 4 945 " --> pdb=" O SER 4 941 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER 4 946 " --> pdb=" O ARG 4 942 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE 4 947 " --> pdb=" O MET 4 943 " (cutoff:3.500A) Processing helix chain '4' and resid 951 through 953 No H-bonds generated for 'chain '4' and resid 951 through 953' Processing helix chain '4' and resid 957 through 969 Processing helix chain '4' and resid 978 through 989 Processing helix chain '4' and resid 996 through 1009 Processing helix chain '4' and resid 1014 through 1030 removed outlier: 3.605A pdb=" N GLN 41030 " --> pdb=" O ARG 41026 " (cutoff:3.500A) Processing helix chain '4' and resid 1035 through 1048 Processing helix chain '4' and resid 1053 through 1058 removed outlier: 3.815A pdb=" N ASN 41058 " --> pdb=" O GLY 41054 " (cutoff:3.500A) Processing helix chain '4' and resid 1060 through 1067 removed outlier: 3.681A pdb=" N SER 41065 " --> pdb=" O ALA 41061 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE 41066 " --> pdb=" O LEU 41062 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 41067 " --> pdb=" O GLY 41063 " (cutoff:3.500A) Processing helix chain '4' and resid 1075 through 1084 Processing helix chain '5' and resid 35 through 51 removed outlier: 3.828A pdb=" N VAL 5 39 " --> pdb=" O ARG 5 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 5 43 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP 5 44 " --> pdb=" O HIS 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 70 Processing helix chain '5' and resid 92 through 107 removed outlier: 5.480A pdb=" N THR 5 96 " --> pdb=" O HIS 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 119 No H-bonds generated for 'chain '5' and resid 116 through 119' Processing helix chain '5' and resid 148 through 157 Processing helix chain '5' and resid 181 through 184 No H-bonds generated for 'chain '5' and resid 181 through 184' Processing helix chain '5' and resid 199 through 209 Processing helix chain '5' and resid 213 through 215 No H-bonds generated for 'chain '5' and resid 213 through 215' Processing helix chain '5' and resid 247 through 256 removed outlier: 3.567A pdb=" N ASP 5 251 " --> pdb=" O GLU 5 247 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA 5 256 " --> pdb=" O SER 5 252 " (cutoff:3.500A) Processing helix chain '5' and resid 266 through 271 Processing helix chain '5' and resid 275 through 278 No H-bonds generated for 'chain '5' and resid 275 through 278' Processing helix chain '6' and resid 63 through 80 Processing helix chain '6' and resid 84 through 96 removed outlier: 3.944A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 118 removed outlier: 3.909A pdb=" N LEU 6 112 " --> pdb=" O SER 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 126 through 132 Processing helix chain '6' and resid 144 through 153 Proline residue: 6 148 - end of helix Processing helix chain '6' and resid 161 through 176 removed outlier: 3.636A pdb=" N VAL 6 165 " --> pdb=" O ASP 6 161 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE 6 166 " --> pdb=" O ALA 6 162 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 6 167 " --> pdb=" O ARG 6 163 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 6 175 " --> pdb=" O GLN 6 171 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN 6 176 " --> pdb=" O LYS 6 172 " (cutoff:3.500A) Processing helix chain '6' and resid 182 through 195 removed outlier: 3.946A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 200 through 215 Processing helix chain '6' and resid 223 through 234 Processing helix chain '6' and resid 239 through 251 Processing helix chain '6' and resid 258 through 271 Proline residue: 6 263 - end of helix removed outlier: 3.717A pdb=" N ILE 6 271 " --> pdb=" O ALA 6 267 " (cutoff:3.500A) Processing helix chain '6' and resid 279 through 287 removed outlier: 3.509A pdb=" N THR 6 284 " --> pdb=" O LYS 6 280 " (cutoff:3.500A) Processing helix chain '6' and resid 295 through 308 Processing helix chain '6' and resid 313 through 323 Processing helix chain '6' and resid 325 through 327 No H-bonds generated for 'chain '6' and resid 325 through 327' Processing helix chain '6' and resid 335 through 345 removed outlier: 3.944A pdb=" N PHE 6 342 " --> pdb=" O THR 6 338 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN 6 343 " --> pdb=" O LEU 6 339 " (cutoff:3.500A) Processing helix chain '6' and resid 350 through 358 Processing helix chain '6' and resid 369 through 380 Processing helix chain '6' and resid 387 through 402 removed outlier: 3.814A pdb=" N ARG 6 392 " --> pdb=" O GLU 6 388 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP 6 402 " --> pdb=" O ALA 6 398 " (cutoff:3.500A) Processing helix chain '6' and resid 406 through 419 Processing helix chain '6' and resid 424 through 434 Processing helix chain '6' and resid 443 through 456 Processing helix chain '6' and resid 461 through 473 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 475 through 480 Processing helix chain '6' and resid 485 through 495 Processing helix chain '6' and resid 501 through 508 Processing sheet with id= A, first strand: chain '1' and resid 169 through 171 Processing sheet with id= B, first strand: chain '1' and resid 315 through 320 removed outlier: 6.485A pdb=" N ASP 1 308 " --> pdb=" O LEU 1 316 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL 1 318 " --> pdb=" O HIS 1 306 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS 1 306 " --> pdb=" O VAL 1 318 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER 1 320 " --> pdb=" O GLN 1 304 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLN 1 304 " --> pdb=" O SER 1 320 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR 1 382 " --> pdb=" O THR 1 297 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS 1 299 " --> pdb=" O LEU 1 380 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU 1 380 " --> pdb=" O LYS 1 299 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU 1 387 " --> pdb=" O LYS 1 407 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG 1 389 " --> pdb=" O GLU 1 405 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN 1 326 " --> pdb=" O LEU 1 342 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER 1 344 " --> pdb=" O ASN 1 324 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASN 1 324 " --> pdb=" O SER 1 344 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 362 through 364 Processing sheet with id= D, first strand: chain '1' and resid 383 through 385 removed outlier: 6.092A pdb=" N GLU 1 385 " --> pdb=" O PRO 1 410 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 175 through 179 removed outlier: 8.834A pdb=" N GLN 2 176 " --> pdb=" O PHE 2 341 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL 2 343 " --> pdb=" O GLN 2 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU 2 178 " --> pdb=" O VAL 2 343 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS 2 345 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL 2 358 " --> pdb=" O PHE 2 341 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL 2 343 " --> pdb=" O TYR 2 356 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR 2 356 " --> pdb=" O VAL 2 343 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS 2 345 " --> pdb=" O LEU 2 354 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU 2 354 " --> pdb=" O HIS 2 345 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP 2 353 " --> pdb=" O GLY 2 246 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG 2 361 " --> pdb=" O PRO 2 238 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR 2 441 " --> pdb=" O ALA 2 245 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS 2 399 " --> pdb=" O LEU 2 427 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 186 through 191 Processing sheet with id= G, first strand: chain '2' and resid 247 through 250 Processing sheet with id= H, first strand: chain '2' and resid 301 through 304 removed outlier: 3.735A pdb=" N GLN 2 303 " --> pdb=" O LYS 2 406 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS 2 406 " --> pdb=" O GLN 2 303 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '5' and resid 57 through 61 Processing sheet with id= J, first strand: chain '5' and resid 76 through 78 Processing sheet with id= K, first strand: chain '5' and resid 131 through 134 removed outlier: 6.373A pdb=" N ASP 5 168 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL 5 140 " --> pdb=" O ASP 5 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE 5 170 " --> pdb=" O VAL 5 140 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS 5 142 " --> pdb=" O PHE 5 170 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU 5 172 " --> pdb=" O HIS 5 142 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 192 through 196 removed outlier: 6.584A pdb=" N ASN 5 218 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR 5 195 " --> pdb=" O ASN 5 218 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL 5 220 " --> pdb=" O THR 5 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '5' and resid 239 through 243 removed outlier: 6.863A pdb=" N ASN 5 259 " --> pdb=" O VAL 5 240 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL 5 242 " --> pdb=" O ASN 5 259 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE 5 261 " --> pdb=" O VAL 5 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 930 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 9.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7318 1.34 - 1.46: 4084 1.46 - 1.58: 11244 1.58 - 1.70: 95 1.70 - 1.82: 191 Bond restraints: 22932 Sorted by residual: bond pdb=" C4 ATP g 201 " pdb=" C5 ATP g 201 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C5 ATP g 201 " pdb=" C6 ATP g 201 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C8 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 2.07e+01 bond pdb=" C5 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 1.374 1.332 0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 22927 not shown) Histogram of bond angle deviations from ideal: 98.81 - 106.23: 792 106.23 - 113.65: 12866 113.65 - 121.07: 11483 121.07 - 128.49: 5965 128.49 - 135.91: 184 Bond angle restraints: 31290 Sorted by residual: angle pdb=" PB ATP g 201 " pdb=" O3B ATP g 201 " pdb=" PG ATP g 201 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP g 201 " pdb=" O3A ATP g 201 " pdb=" PB ATP g 201 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" N3 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 127.04 135.03 -7.99 1.15e+00 7.59e-01 4.84e+01 angle pdb=" N1 ATP g 201 " pdb=" C2 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 128.69 123.63 5.06 1.00e+00 1.00e+00 2.56e+01 ... (remaining 31285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.43: 12745 25.43 - 50.85: 1076 50.85 - 76.28: 136 76.28 - 101.70: 27 101.70 - 127.13: 2 Dihedral angle restraints: 13986 sinusoidal: 5992 harmonic: 7994 Sorted by residual: dihedral pdb=" O4' A g 5 " pdb=" C1' A g 5 " pdb=" N9 A g 5 " pdb=" C4 A g 5 " ideal model delta sinusoidal sigma weight residual -106.00 -167.61 61.61 1 1.70e+01 3.46e-03 1.74e+01 dihedral pdb=" CA ASP 4 862 " pdb=" C ASP 4 862 " pdb=" N LYS 4 863 " pdb=" CA LYS 4 863 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN 5 75 " pdb=" C GLN 5 75 " pdb=" N MET 5 76 " pdb=" CA MET 5 76 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3024 0.051 - 0.103: 523 0.103 - 0.154: 80 0.154 - 0.205: 6 0.205 - 0.256: 2 Chirality restraints: 3635 Sorted by residual: chirality pdb=" CB VAL 4 501 " pdb=" CA VAL 4 501 " pdb=" CG1 VAL 4 501 " pdb=" CG2 VAL 4 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL 1 372 " pdb=" CA VAL 1 372 " pdb=" CG1 VAL 1 372 " pdb=" CG2 VAL 1 372 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE 4 366 " pdb=" N ILE 4 366 " pdb=" C ILE 4 366 " pdb=" CB ILE 4 366 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3632 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 492 " -0.020 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" CG PHE 6 492 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 492 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 492 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 492 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 492 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE 6 492 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 6 489 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C GLU 6 489 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU 6 489 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU 6 490 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 4 361 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C GLU 4 361 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU 4 361 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN 4 362 " 0.012 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1723 2.74 - 3.28: 23466 3.28 - 3.82: 37160 3.82 - 4.36: 40918 4.36 - 4.90: 68643 Nonbonded interactions: 171910 Sorted by model distance: nonbonded pdb=" OG SER 4 525 " pdb=" OE1 GLU 4 528 " model vdw 2.196 2.440 nonbonded pdb=" O LEU 3 370 " pdb=" OG SER 3 374 " model vdw 2.200 2.440 nonbonded pdb=" O ARG 6 281 " pdb=" OG1 THR 6 284 " model vdw 2.235 2.440 nonbonded pdb=" O ARG 41056 " pdb=" OG SER 41060 " model vdw 2.240 2.440 nonbonded pdb=" OD2 ASP 2 124 " pdb=" NH2 ARG 6 235 " model vdw 2.249 2.520 ... (remaining 171905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.870 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 64.420 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 0.080 22932 Z= 0.189 Angle : 0.652 18.302 31290 Z= 0.362 Chirality : 0.040 0.256 3635 Planarity : 0.004 0.043 3880 Dihedral : 17.575 127.130 8780 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.60 % Allowed : 26.07 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2711 helix: 0.91 (0.14), residues: 1502 sheet: 0.02 (0.36), residues: 217 loop : -1.84 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 2 443 HIS 0.005 0.001 HIS 6 475 PHE 0.048 0.001 PHE 6 492 TYR 0.015 0.001 TYR 4 341 ARG 0.008 0.000 ARG 3 415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 103 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7429 (mmt90) REVERT: 5 167 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: 5 265 TRP cc_start: 0.7608 (t-100) cc_final: 0.6314 (m-90) outliers start: 14 outliers final: 5 residues processed: 259 average time/residue: 0.3283 time to fit residues: 134.3789 Evaluate side-chains 235 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 275 LEU Chi-restraints excluded: chain 4 residue 494 LEU Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 6 residue 402 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 160 optimal weight: 0.0870 chunk 249 optimal weight: 1.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 113 GLN 3 277 GLN ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22932 Z= 0.159 Angle : 0.531 10.490 31290 Z= 0.266 Chirality : 0.038 0.179 3635 Planarity : 0.004 0.041 3880 Dihedral : 10.339 124.194 3671 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.14 % Allowed : 24.79 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2711 helix: 1.20 (0.14), residues: 1491 sheet: 0.29 (0.36), residues: 216 loop : -1.82 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 443 HIS 0.006 0.001 HIS 41013 PHE 0.023 0.001 PHE 4 473 TYR 0.015 0.001 TYR 6 507 ARG 0.008 0.000 ARG 2 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 251 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.5780 (pp30) REVERT: 1 455 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (tt) REVERT: 3 170 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7119 (mt) REVERT: 3 173 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8248 (mm) REVERT: 4 564 MET cc_start: 0.8112 (tpp) cc_final: 0.7700 (tpp) REVERT: 4 943 MET cc_start: 0.7442 (tpt) cc_final: 0.7147 (tpt) REVERT: 5 46 TYR cc_start: 0.8142 (t80) cc_final: 0.7895 (t80) REVERT: 5 167 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: 5 265 TRP cc_start: 0.7795 (t-100) cc_final: 0.6486 (m-90) REVERT: 6 505 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8283 (mp10) outliers start: 73 outliers final: 35 residues processed: 307 average time/residue: 0.3086 time to fit residues: 153.1465 Evaluate side-chains 272 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 231 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 455 LEU Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 4 residue 447 CYS Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 670 LEU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 114 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 250 optimal weight: 0.4980 chunk 270 optimal weight: 0.0040 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 200 optimal weight: 0.0030 overall best weight: 0.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 254 GLN ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 113 GLN ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22932 Z= 0.132 Angle : 0.512 9.887 31290 Z= 0.256 Chirality : 0.038 0.189 3635 Planarity : 0.003 0.044 3880 Dihedral : 10.061 123.736 3660 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.14 % Allowed : 25.56 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2711 helix: 1.35 (0.14), residues: 1477 sheet: 0.31 (0.35), residues: 222 loop : -1.76 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 443 HIS 0.005 0.001 HIS 41013 PHE 0.024 0.001 PHE 6 492 TYR 0.023 0.001 TYR 4 341 ARG 0.005 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 261 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.5795 (pp30) REVERT: 1 455 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (tt) REVERT: 2 405 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6605 (ttt-90) REVERT: 3 170 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.6954 (mt) REVERT: 3 173 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8255 (mm) REVERT: 3 183 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6375 (pp) REVERT: 4 448 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7861 (mt-10) REVERT: 4 564 MET cc_start: 0.8005 (tpp) cc_final: 0.7633 (tpp) REVERT: 5 46 TYR cc_start: 0.8139 (t80) cc_final: 0.7813 (t80) REVERT: 5 102 MET cc_start: 0.8118 (tpp) cc_final: 0.7787 (mpp) REVERT: 5 167 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: 5 265 TRP cc_start: 0.7689 (t-100) cc_final: 0.6459 (m-90) REVERT: 6 130 GLU cc_start: 0.8214 (tp30) cc_final: 0.7923 (tp30) REVERT: 6 505 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (mp10) outliers start: 73 outliers final: 30 residues processed: 320 average time/residue: 0.3256 time to fit residues: 168.5581 Evaluate side-chains 280 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 455 LEU Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 405 ARG Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 71 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22932 Z= 0.242 Angle : 0.564 11.600 31290 Z= 0.281 Chirality : 0.039 0.242 3635 Planarity : 0.004 0.076 3880 Dihedral : 10.051 125.069 3660 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.25 % Allowed : 25.17 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2711 helix: 1.18 (0.14), residues: 1482 sheet: 0.14 (0.35), residues: 219 loop : -1.87 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 443 HIS 0.005 0.001 HIS 41013 PHE 0.026 0.001 PHE 6 492 TYR 0.021 0.001 TYR 3 100 ARG 0.010 0.000 ARG 1 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 236 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 405 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6588 (ttt-90) REVERT: 3 170 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8160 (mm) REVERT: 3 173 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8169 (mm) REVERT: 3 183 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6586 (pp) REVERT: 3 474 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: 4 448 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7897 (mt-10) REVERT: 4 564 MET cc_start: 0.7934 (tpp) cc_final: 0.7569 (tpp) REVERT: 4 654 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: 5 46 TYR cc_start: 0.8289 (t80) cc_final: 0.8085 (t80) REVERT: 5 102 MET cc_start: 0.8202 (tpp) cc_final: 0.7840 (mpp) REVERT: 5 265 TRP cc_start: 0.7904 (t-100) cc_final: 0.6617 (m-90) REVERT: 5 273 ILE cc_start: 0.6799 (mm) cc_final: 0.6517 (mm) REVERT: 6 130 GLU cc_start: 0.8365 (tp30) cc_final: 0.8081 (tp30) REVERT: 6 307 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7149 (t80) REVERT: 6 505 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8303 (mp10) outliers start: 99 outliers final: 63 residues processed: 318 average time/residue: 0.2975 time to fit residues: 153.9682 Evaluate side-chains 295 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 224 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 405 ARG Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 184 VAL Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 751 ILE Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 238 ILE Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 197 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 41052 HIS 6 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22932 Z= 0.213 Angle : 0.541 10.339 31290 Z= 0.271 Chirality : 0.039 0.344 3635 Planarity : 0.004 0.041 3880 Dihedral : 9.945 124.272 3657 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.42 % Allowed : 24.79 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2711 helix: 1.15 (0.14), residues: 1481 sheet: 0.11 (0.34), residues: 219 loop : -1.89 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 443 HIS 0.014 0.001 HIS 3 168 PHE 0.026 0.001 PHE 6 492 TYR 0.018 0.001 TYR 5 184 ARG 0.005 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 243 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 183 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6491 (pp) REVERT: 3 474 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: 4 348 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: 4 448 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7813 (mt-10) REVERT: 4 564 MET cc_start: 0.7895 (tpp) cc_final: 0.7552 (tpp) REVERT: 4 654 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: 5 61 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: 5 167 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: 5 265 TRP cc_start: 0.7869 (t-100) cc_final: 0.6605 (m-90) REVERT: 5 273 ILE cc_start: 0.6889 (mm) cc_final: 0.6412 (mm) REVERT: 6 85 MET cc_start: 0.8248 (mmp) cc_final: 0.7949 (mmp) REVERT: 6 130 GLU cc_start: 0.8343 (tp30) cc_final: 0.8087 (tp30) REVERT: 6 307 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7093 (t80) REVERT: 6 505 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8292 (mp10) outliers start: 103 outliers final: 69 residues processed: 327 average time/residue: 0.2988 time to fit residues: 157.7391 Evaluate side-chains 309 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 232 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 323 LEU Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 61 MET Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 184 ASP Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.1980 chunk 239 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 411 ASN 6 457 GLN 6 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22932 Z= 0.185 Angle : 0.538 10.618 31290 Z= 0.267 Chirality : 0.038 0.258 3635 Planarity : 0.004 0.044 3880 Dihedral : 9.887 123.571 3657 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.38 % Allowed : 25.47 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2711 helix: 1.19 (0.14), residues: 1482 sheet: 0.14 (0.34), residues: 219 loop : -1.87 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 443 HIS 0.008 0.001 HIS 3 168 PHE 0.028 0.001 PHE 6 492 TYR 0.016 0.001 TYR 5 184 ARG 0.006 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 240 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 419 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8539 (pp20) REVERT: 2 257 GLN cc_start: 0.6814 (tp40) cc_final: 0.6383 (tp40) REVERT: 3 183 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6416 (pp) REVERT: 3 474 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: 4 348 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: 4 448 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7839 (mt-10) REVERT: 4 564 MET cc_start: 0.7758 (tpp) cc_final: 0.7255 (tpp) REVERT: 4 654 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: 5 167 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: 5 265 TRP cc_start: 0.7766 (t-100) cc_final: 0.6615 (t-100) REVERT: 5 273 ILE cc_start: 0.6946 (mm) cc_final: 0.6478 (mm) REVERT: 6 85 MET cc_start: 0.8255 (mmp) cc_final: 0.7924 (mmp) REVERT: 6 130 GLU cc_start: 0.8309 (tp30) cc_final: 0.8054 (tp30) REVERT: 6 307 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7003 (t80) REVERT: 6 411 ASN cc_start: 0.8889 (m-40) cc_final: 0.8668 (m110) REVERT: 6 505 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8266 (mp10) outliers start: 102 outliers final: 72 residues processed: 325 average time/residue: 0.2957 time to fit residues: 156.7926 Evaluate side-chains 308 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 228 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 444 ILE Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 306 SER Chi-restraints excluded: chain 3 residue 323 LEU Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 GLN ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN 6 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22932 Z= 0.269 Angle : 0.583 10.742 31290 Z= 0.292 Chirality : 0.040 0.309 3635 Planarity : 0.004 0.048 3880 Dihedral : 9.927 123.963 3657 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.55 % Allowed : 25.77 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2711 helix: 1.04 (0.14), residues: 1474 sheet: -0.03 (0.34), residues: 224 loop : -1.90 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 2 443 HIS 0.008 0.001 HIS 3 321 PHE 0.028 0.002 PHE 6 492 TYR 0.022 0.001 TYR 5 184 ARG 0.006 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 230 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 297 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8606 (t) REVERT: 2 257 GLN cc_start: 0.6845 (tp40) cc_final: 0.6461 (tp40) REVERT: 2 362 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8359 (m-70) REVERT: 3 170 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7274 (mt) REVERT: 3 183 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6593 (pp) REVERT: 3 474 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: 4 348 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: 4 380 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: 4 448 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7856 (mt-10) REVERT: 4 564 MET cc_start: 0.7721 (tpp) cc_final: 0.7498 (tpp) REVERT: 4 654 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: 4 824 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7423 (mmm-85) REVERT: 4 873 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8253 (tp) REVERT: 5 167 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: 5 265 TRP cc_start: 0.7952 (t-100) cc_final: 0.6958 (t-100) REVERT: 5 273 ILE cc_start: 0.7138 (mm) cc_final: 0.6730 (mm) REVERT: 6 85 MET cc_start: 0.8336 (mmp) cc_final: 0.8040 (mmp) REVERT: 6 130 GLU cc_start: 0.8339 (tp30) cc_final: 0.8073 (tp30) REVERT: 6 307 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7144 (t80) REVERT: 6 411 ASN cc_start: 0.8861 (m-40) cc_final: 0.8632 (m-40) REVERT: 6 505 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8309 (mp10) outliers start: 106 outliers final: 79 residues processed: 319 average time/residue: 0.3002 time to fit residues: 156.8313 Evaluate side-chains 315 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 223 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 264 THR Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 297 THR Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 121 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 362 HIS Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 444 ILE Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 184 VAL Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 306 SER Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 380 GLU Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 546 LEU Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 824 ARG Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 873 ILE Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 238 ILE Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 184 ASP Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 254 GLN ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 345 HIS ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS 5 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22932 Z= 0.195 Angle : 0.564 14.753 31290 Z= 0.280 Chirality : 0.039 0.259 3635 Planarity : 0.004 0.048 3880 Dihedral : 9.836 122.504 3657 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.38 % Allowed : 26.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2711 helix: 1.11 (0.14), residues: 1477 sheet: 0.04 (0.34), residues: 224 loop : -1.86 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 443 HIS 0.008 0.001 HIS 3 321 PHE 0.030 0.001 PHE 4 473 TYR 0.016 0.001 TYR 5 184 ARG 0.006 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 233 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5709 (pp30) REVERT: 1 297 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8545 (t) REVERT: 1 419 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: 2 257 GLN cc_start: 0.6763 (tp40) cc_final: 0.6428 (tp40) REVERT: 2 291 MET cc_start: 0.8491 (ppp) cc_final: 0.6788 (ttt) REVERT: 2 362 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8347 (m-70) REVERT: 3 183 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6573 (pp) REVERT: 3 439 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6665 (tp) REVERT: 3 474 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: 4 348 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: 4 380 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: 4 448 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7815 (mt-10) REVERT: 4 564 MET cc_start: 0.7654 (tpp) cc_final: 0.7334 (tpp) REVERT: 4 654 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: 4 824 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7511 (mmm-85) REVERT: 4 900 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6264 (p0) REVERT: 5 167 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: 5 265 TRP cc_start: 0.7835 (t-100) cc_final: 0.6923 (t-100) REVERT: 5 273 ILE cc_start: 0.7217 (mm) cc_final: 0.6850 (mm) REVERT: 6 85 MET cc_start: 0.8385 (mmp) cc_final: 0.8065 (mmp) REVERT: 6 130 GLU cc_start: 0.8270 (tp30) cc_final: 0.8026 (tp30) REVERT: 6 307 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6956 (t80) REVERT: 6 411 ASN cc_start: 0.8854 (m-40) cc_final: 0.8616 (m-40) outliers start: 102 outliers final: 70 residues processed: 316 average time/residue: 0.3038 time to fit residues: 155.7026 Evaluate side-chains 310 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 226 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 264 THR Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 297 THR Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 362 HIS Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 444 ILE Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 306 SER Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 439 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 380 GLU Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 824 ARG Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 877 SER Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 184 ASP Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 335 ILE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 0.5980 chunk 253 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 246 optimal weight: 0.0870 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22932 Z= 0.156 Angle : 0.560 14.283 31290 Z= 0.275 Chirality : 0.038 0.259 3635 Planarity : 0.004 0.047 3880 Dihedral : 9.743 121.578 3657 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.57 % Allowed : 27.06 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2711 helix: 1.19 (0.14), residues: 1482 sheet: 0.16 (0.34), residues: 224 loop : -1.81 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 443 HIS 0.009 0.001 HIS 3 321 PHE 0.023 0.001 PHE 6 302 TYR 0.013 0.001 TYR 5 184 ARG 0.007 0.000 ARG 2 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 243 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5643 (pp30) REVERT: 1 419 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8554 (pp20) REVERT: 2 257 GLN cc_start: 0.6727 (tp40) cc_final: 0.6404 (tp40) REVERT: 2 291 MET cc_start: 0.8288 (ppp) cc_final: 0.6851 (ttt) REVERT: 2 362 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8313 (m-70) REVERT: 3 75 ARG cc_start: 0.8585 (tpt170) cc_final: 0.8138 (tpm170) REVERT: 3 173 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8245 (mm) REVERT: 3 183 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6475 (pp) REVERT: 3 439 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6693 (tp) REVERT: 3 474 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: 4 348 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: 4 448 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7707 (mt-10) REVERT: 4 564 MET cc_start: 0.7628 (tpp) cc_final: 0.7373 (tpp) REVERT: 4 652 ILE cc_start: 0.8454 (mm) cc_final: 0.8104 (mt) REVERT: 4 654 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: 4 824 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7571 (mmm-85) REVERT: 4 900 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.6180 (p0) REVERT: 5 167 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: 5 265 TRP cc_start: 0.7771 (t-100) cc_final: 0.6968 (t-100) REVERT: 5 273 ILE cc_start: 0.7250 (mm) cc_final: 0.6873 (mm) REVERT: 6 85 MET cc_start: 0.8363 (mmp) cc_final: 0.8043 (mmp) REVERT: 6 130 GLU cc_start: 0.8278 (tp30) cc_final: 0.8044 (tp30) REVERT: 6 307 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6836 (t80) REVERT: 6 411 ASN cc_start: 0.8874 (m-40) cc_final: 0.8621 (m-40) outliers start: 83 outliers final: 63 residues processed: 310 average time/residue: 0.2999 time to fit residues: 151.0034 Evaluate side-chains 307 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 264 THR Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 362 HIS Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 306 SER Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 439 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 824 ARG Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 184 ASP Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 335 ILE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 252 optimal weight: 0.0370 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22932 Z= 0.186 Angle : 0.574 14.230 31290 Z= 0.281 Chirality : 0.039 0.266 3635 Planarity : 0.004 0.047 3880 Dihedral : 9.702 121.473 3657 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.61 % Allowed : 27.23 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2711 helix: 1.15 (0.14), residues: 1484 sheet: 0.18 (0.34), residues: 224 loop : -1.80 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 443 HIS 0.008 0.001 HIS 41013 PHE 0.023 0.001 PHE 6 302 TYR 0.014 0.001 TYR 5 184 ARG 0.014 0.000 ARG 4 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 233 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5667 (pp30) REVERT: 1 350 ARG cc_start: 0.6467 (ptt180) cc_final: 0.6254 (ptt180) REVERT: 1 419 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8550 (pp20) REVERT: 2 257 GLN cc_start: 0.6749 (tp40) cc_final: 0.6419 (tp40) REVERT: 2 362 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8332 (m-70) REVERT: 3 75 ARG cc_start: 0.8609 (tpt170) cc_final: 0.8175 (tpm170) REVERT: 3 173 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8280 (mm) REVERT: 3 183 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6529 (pp) REVERT: 3 319 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7456 (mmtm) REVERT: 3 439 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6708 (tp) REVERT: 3 474 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: 4 348 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: 4 448 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7837 (mt-10) REVERT: 4 495 CYS cc_start: 0.8296 (m) cc_final: 0.8025 (m) REVERT: 4 564 MET cc_start: 0.7624 (tpp) cc_final: 0.7380 (tpp) REVERT: 4 652 ILE cc_start: 0.8463 (mm) cc_final: 0.8116 (mt) REVERT: 4 654 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: 4 824 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7477 (mmm-85) REVERT: 4 900 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6200 (p0) REVERT: 5 167 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: 5 265 TRP cc_start: 0.7829 (t-100) cc_final: 0.6911 (t-100) REVERT: 5 273 ILE cc_start: 0.7266 (mm) cc_final: 0.6864 (mm) REVERT: 6 85 MET cc_start: 0.8388 (mmp) cc_final: 0.8070 (mmp) REVERT: 6 130 GLU cc_start: 0.8294 (tp30) cc_final: 0.8050 (tp30) REVERT: 6 307 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6766 (t80) outliers start: 84 outliers final: 67 residues processed: 300 average time/residue: 0.3056 time to fit residues: 149.6592 Evaluate side-chains 310 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 230 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 226 ASP Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 264 THR Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 292 LEU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 266 THR Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 362 HIS Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 444 ILE Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 306 SER Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 3 residue 439 LEU Chi-restraints excluded: chain 3 residue 474 GLU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 797 VAL Chi-restraints excluded: chain 4 residue 824 ARG Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 900 ASP Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 4 residue 1085 LEU Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 238 ILE Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 184 ASP Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 232 SER Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 335 ILE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 224 optimal weight: 0.0170 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 113 GLN ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.141263 restraints weight = 44401.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.139166 restraints weight = 55131.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140706 restraints weight = 49181.939| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22932 Z= 0.157 Angle : 0.576 14.280 31290 Z= 0.280 Chirality : 0.039 0.266 3635 Planarity : 0.004 0.050 3880 Dihedral : 9.622 120.552 3657 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.61 % Allowed : 27.28 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2711 helix: 1.19 (0.14), residues: 1475 sheet: 0.24 (0.34), residues: 226 loop : -1.78 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 443 HIS 0.007 0.001 HIS 41013 PHE 0.034 0.001 PHE 4 473 TYR 0.012 0.001 TYR 5 184 ARG 0.012 0.000 ARG 4 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.04 seconds wall clock time: 75 minutes 45.18 seconds (4545.18 seconds total)