Starting phenix.real_space_refine on Mon Mar 18 06:20:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nue_0519/03_2024/6nue_0519_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.135 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 42 5.49 5 S 39 5.16 5 C 12690 2.51 5 N 3403 2.21 5 O 4001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 28": "NH1" <-> "NH2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "J ARG 383": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J ARG 421": "NH1" <-> "NH2" Residue "J ARG 515": "NH1" <-> "NH2" Residue "J ARG 531": "NH1" <-> "NH2" Residue "J TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 678": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "M ARG 65": "NH1" <-> "NH2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 171": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P ARG 171": "NH1" <-> "NH2" Residue "P ARG 188": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 5928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5928 Classifications: {'peptide': 733} Link IDs: {'PTRANS': 8, 'TRANS': 724} Chain breaks: 1 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "B" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "C" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 832 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 18} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "N" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" 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: 9.99, per 1000 atoms: 0.50 Number of scatterers: 20175 At special positions: 0 Unit cell: (94.34, 120.84, 208.82, 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 39 16.00 P 42 15.00 O 4001 8.00 N 3403 7.00 C 12690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 3.5 seconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 15 sheets defined 30.4% alpha, 6.4% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'J' and resid 6 through 13 removed outlier: 3.600A pdb=" N TYR J 10 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 13 " --> pdb=" O PHE J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 31 through 42 removed outlier: 3.522A pdb=" N GLY J 35 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE J 42 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 53 removed outlier: 3.638A pdb=" N GLN J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE J 52 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 47 through 53' Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.547A pdb=" N ASN J 78 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 153 through 158 Processing helix chain 'J' and resid 174 through 177 No H-bonds generated for 'chain 'J' and resid 174 through 177' Processing helix chain 'J' and resid 181 through 183 No H-bonds generated for 'chain 'J' and resid 181 through 183' Processing helix chain 'J' and resid 198 through 218 removed outlier: 3.721A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA J 207 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA J 209 " --> pdb=" O THR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 289 removed outlier: 3.673A pdb=" N ALA J 264 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS J 265 " --> pdb=" O GLY J 262 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN J 266 " --> pdb=" O ALA J 263 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU J 267 " --> pdb=" O ALA J 264 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS J 268 " --> pdb=" O LYS J 265 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU J 272 " --> pdb=" O ALA J 269 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU J 274 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP J 275 " --> pdb=" O LEU J 272 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE J 276 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET J 277 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 278 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE J 281 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER J 284 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU J 285 " --> pdb=" O ALA J 282 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU J 286 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP J 287 " --> pdb=" O SER J 284 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 288 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 289 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 325 removed outlier: 3.719A pdb=" N GLU J 316 " --> pdb=" O GLU J 312 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN J 320 " --> pdb=" O GLU J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 331 No H-bonds generated for 'chain 'J' and resid 328 through 331' Processing helix chain 'J' and resid 348 through 350 No H-bonds generated for 'chain 'J' and resid 348 through 350' Processing helix chain 'J' and resid 358 through 375 removed outlier: 4.093A pdb=" N ILE J 364 " --> pdb=" O SER J 360 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR J 365 " --> pdb=" O TYR J 361 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA J 368 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG J 370 " --> pdb=" O GLN J 366 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET J 371 " --> pdb=" O LYS J 367 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 372 " --> pdb=" O ALA J 368 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER J 373 " --> pdb=" O SER J 369 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU J 374 " --> pdb=" O ARG J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 388 No H-bonds generated for 'chain 'J' and resid 385 through 388' Processing helix chain 'J' and resid 422 through 427 Processing helix chain 'J' and resid 496 through 499 No H-bonds generated for 'chain 'J' and resid 496 through 499' Processing helix chain 'J' and resid 540 through 554 removed outlier: 4.254A pdb=" N PHE J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER J 547 " --> pdb=" O SER J 543 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 548 " --> pdb=" O ALA J 544 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 552 " --> pdb=" O ARG J 548 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE J 553 " --> pdb=" O SER J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 557 through 561 Processing helix chain 'J' and resid 583 through 601 removed outlier: 3.780A pdb=" N ILE J 587 " --> pdb=" O TRP J 583 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 591 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU J 592 " --> pdb=" O ALA J 588 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 594 " --> pdb=" O THR J 590 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS J 599 " --> pdb=" O GLN J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 635 removed outlier: 4.050A pdb=" N THR J 627 " --> pdb=" O MET J 623 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY J 628 " --> pdb=" O ALA J 624 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU J 630 " --> pdb=" O GLN J 626 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU J 632 " --> pdb=" O GLY J 628 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS J 635 " --> pdb=" O GLU J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 654 through 657 No H-bonds generated for 'chain 'J' and resid 654 through 657' Processing helix chain 'J' and resid 660 through 663 No H-bonds generated for 'chain 'J' and resid 660 through 663' Processing helix chain 'J' and resid 665 through 671 removed outlier: 3.851A pdb=" N ARG J 669 " --> pdb=" O LEU J 665 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 691 removed outlier: 4.148A pdb=" N GLU J 688 " --> pdb=" O TYR J 684 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG J 691 " --> pdb=" O ILE J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 713 removed outlier: 3.510A pdb=" N ALA J 702 " --> pdb=" O LYS J 698 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA J 705 " --> pdb=" O VAL J 701 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR J 706 " --> pdb=" O ALA J 702 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR J 707 " --> pdb=" O ARG J 703 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 708 " --> pdb=" O LEU J 704 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR J 709 " --> pdb=" O ALA J 705 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 711 " --> pdb=" O TYR J 707 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU J 712 " --> pdb=" O LEU J 708 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 721 removed outlier: 3.740A pdb=" N ASP J 721 " --> pdb=" O ASP J 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 718 through 721' Processing helix chain 'J' and resid 726 through 732 Processing helix chain 'J' and resid 738 through 754 removed outlier: 3.879A pdb=" N LYS J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU J 743 " --> pdb=" O SER J 739 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA J 744 " --> pdb=" O ASP J 740 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU J 745 " --> pdb=" O ARG J 741 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU J 746 " --> pdb=" O LYS J 742 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL J 752 " --> pdb=" O LEU J 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.840A pdb=" N ASP A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.856A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.918A pdb=" N ASP A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.927A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.596A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.609A pdb=" N CYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 removed outlier: 3.816A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.890A pdb=" N ASP B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 removed outlier: 4.023A pdb=" N LYS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.568A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'C' and resid 50 through 60 removed outlier: 4.060A pdb=" N THR C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.758A pdb=" N LYS C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.077A pdb=" N THR E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 83 removed outlier: 4.250A pdb=" N ARG E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 83' Processing helix chain 'E' and resid 105 through 112 removed outlier: 3.621A pdb=" N GLU E 108 " --> pdb=" O ASN E 105 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 109 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 111 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 179 removed outlier: 3.724A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 175 " --> pdb=" O ARG E 171 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 179 " --> pdb=" O LYS E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'I' and resid 29 through 43 removed outlier: 3.805A pdb=" N PHE I 33 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER I 34 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU I 36 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL I 37 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU I 39 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU I 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 53 removed outlier: 3.504A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 4.069A pdb=" N LYS I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU I 99 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 166 through 169 No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 226 through 229 No H-bonds generated for 'chain 'I' and resid 226 through 229' Processing helix chain 'M' and resid 38 through 41 No H-bonds generated for 'chain 'M' and resid 38 through 41' Processing helix chain 'M' and resid 43 through 49 removed outlier: 3.670A pdb=" N ASP M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.854A pdb=" N SER M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 85 removed outlier: 3.917A pdb=" N ASP M 80 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 93 removed outlier: 3.968A pdb=" N LYS M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 117 removed outlier: 3.601A pdb=" N ARG M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS M 104 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 111 " --> pdb=" O MET M 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS M 115 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR M 117 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 60 removed outlier: 3.535A pdb=" N LYS N 55 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR N 58 " --> pdb=" O GLY N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.231A pdb=" N ARG N 81 " --> pdb=" O ASP N 77 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU N 82 " --> pdb=" O ILE N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'N' and resid 105 through 109 removed outlier: 3.571A pdb=" N GLU N 108 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU N 109 " --> pdb=" O ALA N 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 105 through 109' Processing helix chain 'N' and resid 163 through 178 removed outlier: 3.877A pdb=" N LYS N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'O' and resid 50 through 56 removed outlier: 3.771A pdb=" N GLY O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 removed outlier: 4.357A pdb=" N ARG O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU O 82 " --> pdb=" O ILE O 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 83' Processing helix chain 'O' and resid 105 through 112 removed outlier: 3.629A pdb=" N GLU O 108 " --> pdb=" O ASN O 105 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU O 109 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP O 110 " --> pdb=" O ASP O 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER O 111 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 179 removed outlier: 3.743A pdb=" N LYS O 168 " --> pdb=" O GLU O 164 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 169 " --> pdb=" O GLU O 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS O 175 " --> pdb=" O ARG O 171 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 removed outlier: 4.373A pdb=" N THR P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 83 removed outlier: 4.294A pdb=" N ARG P 81 " --> pdb=" O ASP P 77 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 77 through 83' Processing helix chain 'P' and resid 105 through 107 No H-bonds generated for 'chain 'P' and resid 105 through 107' Processing helix chain 'P' and resid 110 through 112 No H-bonds generated for 'chain 'P' and resid 110 through 112' Processing helix chain 'P' and resid 163 through 179 removed outlier: 3.745A pdb=" N LYS P 168 " --> pdb=" O GLU P 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS P 175 " --> pdb=" O ARG P 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU P 179 " --> pdb=" O LYS P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 188 No H-bonds generated for 'chain 'P' and resid 186 through 188' Processing sheet with id= A, first strand: chain 'J' and resid 341 through 346 removed outlier: 4.027A pdb=" N PHE J 346 " --> pdb=" O PHE J 241 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE J 241 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 611 through 614 removed outlier: 3.770A pdb=" N LEU J 511 " --> pdb=" O PHE J 614 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY J 581 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE J 580 " --> pdb=" O SER J 568 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 149 through 154 Processing sheet with id= D, first strand: chain 'C' and resid 11 through 14 Processing sheet with id= E, first strand: chain 'C' and resid 118 through 122 Processing sheet with id= F, first strand: chain 'E' and resid 5 through 11 Processing sheet with id= G, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.739A pdb=" N GLU E 119 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 190 through 192 removed outlier: 4.146A pdb=" N GLU I 190 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR I 9 " --> pdb=" O GLU I 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS I 4 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE I 64 " --> pdb=" O TYR I 157 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 71 through 73 Processing sheet with id= J, first strand: chain 'I' and resid 126 through 134 removed outlier: 4.208A pdb=" N VAL I 127 " --> pdb=" O ARG I 149 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG I 149 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP I 129 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 148 through 154 Processing sheet with id= L, first strand: chain 'N' and resid 121 through 123 removed outlier: 3.584A pdb=" N GLU N 123 " --> pdb=" O ARG N 136 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 5 through 11 Processing sheet with id= N, first strand: chain 'P' and resid 5 through 10 Processing sheet with id= O, first strand: chain 'P' and resid 118 through 122 removed outlier: 3.814A pdb=" N GLU P 119 " --> pdb=" O ARG P 140 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 8.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5945 1.33 - 1.45: 3242 1.45 - 1.57: 11268 1.57 - 1.69: 83 1.69 - 1.81: 66 Bond restraints: 20604 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 20599 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.77: 586 107.77 - 114.87: 12269 114.87 - 121.97: 10762 121.97 - 129.07: 4225 129.07 - 136.16: 65 Bond angle restraints: 27907 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 119.60 20.27 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.19 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 134.99 -7.95 1.15e+00 7.59e-01 4.80e+01 angle pdb=" C SER J 353 " pdb=" CA SER J 353 " pdb=" CB SER J 353 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.52e+01 ... (remaining 27902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 12361 35.22 - 70.43: 160 70.43 - 105.65: 18 105.65 - 140.87: 0 140.87 - 176.08: 9 Dihedral angle restraints: 12548 sinusoidal: 5516 harmonic: 7032 Sorted by residual: dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 51.91 148.09 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' C H 40 " pdb=" C1' C H 40 " pdb=" N1 C H 40 " pdb=" C2 C H 40 " ideal model delta sinusoidal sigma weight residual 200.00 54.87 145.13 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' C H 34 " pdb=" C1' C H 34 " pdb=" N1 C H 34 " pdb=" C2 C H 34 " ideal model delta sinusoidal sigma weight residual 200.00 55.25 144.75 1 1.50e+01 4.44e-03 7.75e+01 ... (remaining 12545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1880 0.027 - 0.053: 883 0.053 - 0.080: 198 0.080 - 0.106: 107 0.106 - 0.133: 46 Chirality restraints: 3114 Sorted by residual: chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" C1' C H 34 " pdb=" O4' C H 34 " pdb=" C2' C H 34 " pdb=" N1 C H 34 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" C1' U H 22 " pdb=" O4' U H 22 " pdb=" C2' U H 22 " pdb=" N1 U H 22 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3111 not shown) Planarity restraints: 3457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO I 197 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 142 " -0.014 5.00e-02 4.00e+02 2.09e-02 7.00e-01 pdb=" N PRO J 143 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO J 143 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 143 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 71 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.95e-01 pdb=" N PRO O 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 72 " -0.012 5.00e-02 4.00e+02 ... (remaining 3454 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2273 2.75 - 3.29: 18917 3.29 - 3.83: 30366 3.83 - 4.36: 35928 4.36 - 4.90: 61509 Nonbonded interactions: 148993 Sorted by model distance: nonbonded pdb=" OG SER I 28 " pdb=" OD1 ASP I 30 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR I 59 " pdb=" OH TYR I 289 " model vdw 2.263 2.440 nonbonded pdb=" O LEU I 60 " pdb=" OH TYR I 289 " model vdw 2.286 2.440 nonbonded pdb=" OG SER J 500 " pdb=" O ILE J 508 " model vdw 2.298 2.440 nonbonded pdb=" O2' C H 12 " pdb=" OP1 G H 13 " model vdw 2.299 2.440 ... (remaining 148988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.110 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.460 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 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 : 0.002 0.083 20604 Z= 0.110 Angle : 0.469 20.272 27907 Z= 0.323 Chirality : 0.036 0.133 3114 Planarity : 0.002 0.024 3457 Dihedral : 12.108 176.083 8020 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 2.38 % Allowed : 15.31 % Favored : 82.30 % Rotamer: Outliers : 0.34 % Allowed : 5.82 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -5.57 (0.12), residues: 2390 helix: -4.37 (0.08), residues: 690 sheet: -3.08 (0.28), residues: 225 loop : -3.64 (0.13), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 583 HIS 0.002 0.000 HIS J 68 PHE 0.006 0.000 PHE J 229 TYR 0.005 0.000 TYR J 670 ARG 0.002 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 603 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7881 (t0) cc_final: 0.7456 (m-30) REVERT: B 87 ILE cc_start: 0.7705 (mm) cc_final: 0.7410 (mt) REVERT: C 99 ARG cc_start: 0.6722 (ttt-90) cc_final: 0.6506 (mmt-90) REVERT: I 234 TYR cc_start: 0.6949 (p90) cc_final: 0.6705 (p90) REVERT: O 44 ILE cc_start: 0.8222 (mm) cc_final: 0.7766 (mm) REVERT: O 68 VAL cc_start: 0.5740 (t) cc_final: 0.5480 (m) outliers start: 7 outliers final: 0 residues processed: 608 average time/residue: 0.3658 time to fit residues: 320.7909 Evaluate side-chains 290 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 218 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 51 GLN J 68 HIS J 106 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 ASN J 223 ASN J 266 GLN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 GLN J 334 GLN J 389 ASN J 403 HIS J 432 HIS ** J 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN J 502 ASN J 560 GLN J 602 ASN J 737 ASN A 27 ASN B 27 ASN C 11 GLN C 85 ASN C 105 ASN C 134 ASN C 213 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 206 ASN E 213 ASN I 83 GLN I 207 ASN I 284 HIS M 27 ASN M 71 GLN N 11 GLN ** N 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN N 213 ASN O 11 GLN ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 213 ASN P 11 GLN P 85 ASN P 105 ASN P 134 ASN P 213 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20604 Z= 0.156 Angle : 0.568 10.513 27907 Z= 0.290 Chirality : 0.041 0.165 3114 Planarity : 0.003 0.036 3457 Dihedral : 12.438 176.857 3278 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.08 % Favored : 89.62 % Rotamer: Outliers : 2.60 % Allowed : 12.75 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.13), residues: 2390 helix: -2.94 (0.14), residues: 701 sheet: -2.29 (0.27), residues: 274 loop : -3.53 (0.13), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 733 HIS 0.006 0.001 HIS J 412 PHE 0.026 0.001 PHE J 672 TYR 0.028 0.001 TYR J 706 ARG 0.006 0.000 ARG N 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 368 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 266 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: A 60 ASP cc_start: 0.7804 (t0) cc_final: 0.7541 (m-30) REVERT: B 87 ILE cc_start: 0.7492 (mm) cc_final: 0.7094 (mt) REVERT: B 92 LYS cc_start: 0.7269 (mtmm) cc_final: 0.6987 (mtmm) REVERT: C 87 LYS cc_start: 0.5943 (mmtt) cc_final: 0.5371 (ttpt) REVERT: C 99 ARG cc_start: 0.6819 (ttt-90) cc_final: 0.6600 (mmt-90) REVERT: C 147 PHE cc_start: 0.5710 (m-80) cc_final: 0.5386 (m-80) REVERT: E 166 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: I 57 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6988 (pttt) REVERT: O 68 VAL cc_start: 0.6481 (t) cc_final: 0.6241 (m) outliers start: 54 outliers final: 23 residues processed: 398 average time/residue: 0.3433 time to fit residues: 202.5558 Evaluate side-chains 311 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 418 ASP Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 560 GLN Chi-restraints excluded: chain J residue 621 SER Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN ** J 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN C 206 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 233 HIS M 67 GLN N 105 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN N 137 GLN P 11 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20604 Z= 0.227 Angle : 0.623 16.093 27907 Z= 0.316 Chirality : 0.043 0.158 3114 Planarity : 0.004 0.074 3457 Dihedral : 12.823 179.801 3278 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.58 % Favored : 90.21 % Rotamer: Outliers : 3.08 % Allowed : 14.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.14), residues: 2390 helix: -2.03 (0.17), residues: 700 sheet: -1.73 (0.27), residues: 308 loop : -3.21 (0.14), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 600 HIS 0.006 0.001 HIS J 412 PHE 0.033 0.002 PHE J 645 TYR 0.019 0.002 TYR B 63 ARG 0.018 0.001 ARG P 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 266 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: J 386 MET cc_start: 0.6312 (mmt) cc_final: 0.5970 (mmt) REVERT: J 602 ASN cc_start: 0.7491 (t0) cc_final: 0.7180 (t0) REVERT: J 661 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5667 (m-80) REVERT: B 97 ARG cc_start: 0.6970 (ttt-90) cc_final: 0.6722 (ttp-170) REVERT: E 204 PHE cc_start: 0.3642 (OUTLIER) cc_final: 0.2687 (m-80) REVERT: I 8 MET cc_start: 0.7560 (ptt) cc_final: 0.7281 (ptt) REVERT: I 294 PHE cc_start: 0.6807 (m-10) cc_final: 0.6585 (m-80) REVERT: O 117 TYR cc_start: 0.7780 (m-80) cc_final: 0.7567 (m-80) REVERT: P 109 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5319 (mp) outliers start: 64 outliers final: 31 residues processed: 353 average time/residue: 0.3614 time to fit residues: 189.9706 Evaluate side-chains 272 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 661 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 SER Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 201 HIS J 266 GLN J 334 GLN J 412 HIS ** J 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN J 667 GLN ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 ASN ** N 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN O 134 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 ASN P 206 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20604 Z= 0.366 Angle : 0.756 13.763 27907 Z= 0.385 Chirality : 0.047 0.215 3114 Planarity : 0.005 0.065 3457 Dihedral : 13.434 175.630 3278 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.66 % Favored : 91.13 % Rotamer: Outliers : 4.04 % Allowed : 15.78 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.15), residues: 2390 helix: -2.01 (0.17), residues: 738 sheet: -1.76 (0.25), residues: 362 loop : -3.15 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 600 HIS 0.010 0.002 HIS J 68 PHE 0.030 0.003 PHE I 294 TYR 0.029 0.003 TYR A 63 ARG 0.020 0.001 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 312 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: C 211 THR cc_start: 0.4111 (OUTLIER) cc_final: 0.3855 (t) REVERT: E 166 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: N 156 THR cc_start: 0.6715 (OUTLIER) cc_final: 0.6484 (p) REVERT: N 198 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (tp) REVERT: P 109 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6200 (mp) outliers start: 84 outliers final: 42 residues processed: 374 average time/residue: 0.3397 time to fit residues: 193.6112 Evaluate side-chains 280 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 146 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 198 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 209 optimal weight: 0.0570 chunk 58 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 536 GLN J 560 GLN A 101 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS E 137 GLN I 152 ASN N 85 ASN O 105 ASN O 159 ASN P 85 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20604 Z= 0.146 Angle : 0.554 8.964 27907 Z= 0.282 Chirality : 0.040 0.172 3114 Planarity : 0.003 0.056 3457 Dihedral : 13.184 175.426 3278 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 3.18 % Allowed : 18.72 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.15), residues: 2390 helix: -1.47 (0.18), residues: 745 sheet: -1.78 (0.24), residues: 376 loop : -2.90 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 PHE 0.018 0.001 PHE O 26 TYR 0.032 0.001 TYR J 468 ARG 0.012 0.001 ARG J 691 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 257 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 THR cc_start: 0.4028 (OUTLIER) cc_final: 0.3815 (t) REVERT: E 93 MET cc_start: 0.7451 (mmm) cc_final: 0.7106 (mmm) REVERT: I 123 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6284 (pt0) REVERT: O 91 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.5962 (p90) REVERT: P 109 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5858 (mp) outliers start: 66 outliers final: 36 residues processed: 301 average time/residue: 0.3089 time to fit residues: 144.4281 Evaluate side-chains 264 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 159 ASN Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 ASN Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 chunk 233 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 266 GLN J 482 HIS A 101 GLN E 206 ASN I 152 ASN N 134 ASN O 105 ASN P 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20604 Z= 0.181 Angle : 0.550 14.231 27907 Z= 0.277 Chirality : 0.041 0.260 3114 Planarity : 0.003 0.059 3457 Dihedral : 13.195 176.868 3278 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 3.42 % Allowed : 19.01 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.16), residues: 2390 helix: -1.12 (0.19), residues: 751 sheet: -1.65 (0.24), residues: 374 loop : -2.82 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 600 HIS 0.003 0.001 HIS J 55 PHE 0.016 0.001 PHE I 294 TYR 0.028 0.001 TYR J 298 ARG 0.009 0.000 ARG J 691 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 259 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 MET cc_start: 0.7541 (mmm) cc_final: 0.7267 (mmm) REVERT: I 123 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6546 (pt0) REVERT: O 91 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6029 (p90) REVERT: O 175 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7792 (tmmt) REVERT: P 109 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6130 (mp) outliers start: 71 outliers final: 49 residues processed: 310 average time/residue: 0.3125 time to fit residues: 148.9070 Evaluate side-chains 281 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 159 ASN Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 145 SER Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 chunk 170 optimal weight: 0.0270 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN N 162 GLN P 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.8145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20604 Z= 0.133 Angle : 0.510 11.570 27907 Z= 0.257 Chirality : 0.039 0.184 3114 Planarity : 0.003 0.064 3457 Dihedral : 13.143 179.482 3278 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 2.60 % Allowed : 20.31 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.16), residues: 2390 helix: -0.82 (0.19), residues: 747 sheet: -1.35 (0.25), residues: 364 loop : -2.69 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 38 HIS 0.003 0.001 HIS J 15 PHE 0.020 0.001 PHE J 645 TYR 0.027 0.001 TYR J 298 ARG 0.008 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.5282 (mp0) REVERT: M 47 ASP cc_start: 0.7296 (p0) cc_final: 0.6809 (p0) REVERT: N 158 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: N 198 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8157 (tp) REVERT: O 91 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6064 (p90) outliers start: 54 outliers final: 40 residues processed: 286 average time/residue: 0.3362 time to fit residues: 149.5203 Evaluate side-chains 273 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 229 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 159 ASN Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 145 SER Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 158 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN M 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.8637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20604 Z= 0.203 Angle : 0.564 10.899 27907 Z= 0.284 Chirality : 0.041 0.190 3114 Planarity : 0.003 0.057 3457 Dihedral : 13.296 176.328 3278 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.12 % Favored : 91.76 % Rotamer: Outliers : 3.22 % Allowed : 20.45 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.16), residues: 2390 helix: -0.78 (0.19), residues: 749 sheet: -1.24 (0.27), residues: 331 loop : -2.60 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 600 HIS 0.004 0.001 HIS J 482 PHE 0.019 0.001 PHE I 294 TYR 0.031 0.002 TYR J 298 ARG 0.007 0.001 ARG J 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 242 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: N 91 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7569 (p90) REVERT: N 158 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: N 198 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8178 (tp) REVERT: O 91 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6578 (p90) outliers start: 67 outliers final: 53 residues processed: 292 average time/residue: 0.3006 time to fit residues: 136.6942 Evaluate side-chains 274 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 216 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 569 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 641 SER Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 159 ASN Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 145 SER Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.8783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20604 Z= 0.166 Angle : 0.545 17.820 27907 Z= 0.272 Chirality : 0.041 0.286 3114 Planarity : 0.003 0.058 3457 Dihedral : 13.297 177.518 3278 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.99 % Favored : 92.85 % Rotamer: Outliers : 2.69 % Allowed : 21.37 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2390 helix: -0.67 (0.19), residues: 760 sheet: -1.21 (0.28), residues: 329 loop : -2.52 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 38 HIS 0.003 0.001 HIS J 55 PHE 0.015 0.001 PHE I 294 TYR 0.032 0.001 TYR M 63 ARG 0.007 0.000 ARG J 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 232 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8482 (mt0) cc_final: 0.8222 (mt0) REVERT: C 139 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.5596 (mp0) REVERT: N 91 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7640 (p90) REVERT: N 158 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6179 (mp0) REVERT: O 91 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6892 (p90) outliers start: 56 outliers final: 49 residues processed: 274 average time/residue: 0.3125 time to fit residues: 132.6694 Evaluate side-chains 275 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 145 SER Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 117 optimal weight: 0.0040 chunk 151 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.8863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20604 Z= 0.154 Angle : 0.530 9.194 27907 Z= 0.268 Chirality : 0.040 0.274 3114 Planarity : 0.003 0.057 3457 Dihedral : 13.288 178.258 3278 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 2.60 % Allowed : 21.70 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.17), residues: 2390 helix: -0.52 (0.19), residues: 757 sheet: -1.22 (0.27), residues: 333 loop : -2.45 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 PHE 0.017 0.001 PHE E 204 TYR 0.034 0.001 TYR M 63 ARG 0.005 0.000 ARG I 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 6 ILE cc_start: 0.8508 (tt) cc_final: 0.8247 (tt) REVERT: A 53 LYS cc_start: 0.8103 (mttp) cc_final: 0.7729 (ptmt) REVERT: A 86 GLN cc_start: 0.8479 (mt0) cc_final: 0.8215 (mt0) REVERT: C 139 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: N 158 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: O 91 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6843 (p90) outliers start: 54 outliers final: 47 residues processed: 277 average time/residue: 0.3124 time to fit residues: 133.7957 Evaluate side-chains 274 residues out of total 2078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 159 ASN Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 161 ASN Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 145 SER Chi-restraints excluded: chain P residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 80 optimal weight: 0.0060 chunk 196 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 168 optimal weight: 0.0040 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143047 restraints weight = 30871.376| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.76 r_work: 0.3742 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20604 Z= 0.127 Angle : 0.503 8.860 27907 Z= 0.254 Chirality : 0.039 0.228 3114 Planarity : 0.003 0.055 3457 Dihedral : 13.247 179.128 3278 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 2.50 % Allowed : 21.80 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2390 helix: -0.25 (0.20), residues: 748 sheet: -1.20 (0.27), residues: 338 loop : -2.35 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 PHE 0.013 0.001 PHE J 726 TYR 0.029 0.001 TYR M 63 ARG 0.005 0.000 ARG I 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.67 seconds wall clock time: 82 minutes 57.60 seconds (4977.60 seconds total)