Starting phenix.real_space_refine on Sat Feb 17 03:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/02_2024/7krn_23007_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.110 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: 9 Type Number sf(0) Gaussians Zn 5 6.06 5 Al 1 5.89 5 P 84 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 10706 2.51 5 N 2921 2.21 5 O 3512 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E ARG 497": "NH1" <-> "NH2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17351 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 30, 'TRANS': 896} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 24.801 57.488 117.421 1.00 23.89 S ATOM 2495 SG CYS A 306 25.661 58.983 120.940 1.00 20.38 S ATOM 2527 SG CYS A 310 26.473 55.387 120.007 1.00 25.02 S ATOM 3935 SG CYS A 487 27.689 71.479 102.359 1.00 28.29 S ATOM 5188 SG CYS A 645 27.498 73.678 105.435 1.00 42.03 S ATOM 5194 SG CYS A 646 25.493 70.452 105.116 1.00 38.20 S ATOM 10924 SG CYS E 5 63.272 63.773 46.080 1.00 47.16 S ATOM 10945 SG CYS E 8 66.887 63.723 46.333 1.00 56.81 S ATOM 11083 SG CYS E 26 65.226 67.169 45.966 1.00 51.99 S ATOM 11104 SG CYS E 29 65.351 65.094 43.058 1.00 60.26 S ATOM 11269 SG CYS E 50 46.464 84.026 46.253 1.00 77.79 S ATOM 11299 SG CYS E 55 43.702 84.328 43.617 1.00 83.82 S ATOM 11432 SG CYS E 72 47.041 85.957 42.987 1.00 81.14 S ATOM 11006 SG CYS E 16 54.162 67.018 41.421 1.00 48.57 S ATOM 11021 SG CYS E 19 53.451 63.374 40.297 1.00 55.15 S Time building chain proxies: 10.11, per 1000 atoms: 0.58 Number of scatterers: 17351 At special positions: 0 Unit cell: (94.785, 160.815, 177.855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 5 29.99 S 117 16.00 P 84 15.00 Al 1 13.00 Mg 2 11.99 F 3 9.00 O 3512 8.00 N 2921 7.00 C 10706 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: 7.27 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " Number of angles added : 16 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 17 sheets defined 38.7% alpha, 8.8% beta 33 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 8.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.636A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.867A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.743A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.838A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.432A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.963A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.496A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.698A pdb=" N TYR A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 654 " --> pdb=" O HIS A 650 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 708 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.944A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 859 through 869 Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 878 through 902 removed outlier: 4.160A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.867A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 removed outlier: 4.141A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.675A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.931A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.828A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.573A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 33 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.988A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 Processing helix chain 'D' and resid 103 through 112 removed outlier: 4.336A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.523A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.689A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 264 removed outlier: 4.255A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 266 through 274 Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.717A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 381 through 389 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 446 through 455 removed outlier: 3.574A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 498 removed outlier: 3.741A pdb=" N GLY E 494 " --> pdb=" O ARG E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'E' and resid 523 through 526 No H-bonds generated for 'chain 'E' and resid 523 through 526' Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.933A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 99 through 105 Processing sheet with id= E, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.762A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= G, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= H, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.278A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= J, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= K, first strand: chain 'B' and resid 127 through 130 removed outlier: 6.144A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.326A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 151 through 153 Processing sheet with id= O, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.743A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 305 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.460A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 480 through 482 524 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4674 1.33 - 1.45: 3903 1.45 - 1.58: 8919 1.58 - 1.70: 213 1.70 - 1.82: 175 Bond restraints: 17884 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.635 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.628 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 17879 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.43: 678 105.43 - 113.11: 9986 113.11 - 120.79: 8533 120.79 - 128.47: 5293 128.47 - 136.14: 182 Bond angle restraints: 24672 Sorted by residual: angle pdb=" N TRP B 182 " pdb=" CA TRP B 182 " pdb=" C TRP B 182 " ideal model delta sigma weight residual 109.81 120.09 -10.28 2.21e+00 2.05e-01 2.17e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 119.65 -9.84 2.21e+00 2.05e-01 1.98e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 119.06 -5.36 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.74 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 24667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 10371 29.04 - 58.08: 476 58.08 - 87.12: 110 87.12 - 116.15: 17 116.15 - 145.19: 8 Dihedral angle restraints: 10982 sinusoidal: 5162 harmonic: 5820 Sorted by residual: dihedral pdb=" CA ALA B 181 " pdb=" C ALA B 181 " pdb=" N TRP B 182 " pdb=" CA TRP B 182 " ideal model delta harmonic sigma weight residual 180.00 -145.50 -34.50 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ALA D 181 " pdb=" C ALA D 181 " pdb=" N TRP D 182 " pdb=" CA TRP D 182 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 10979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.041: 2874 1.041 - 2.082: 0 2.082 - 3.123: 0 3.123 - 4.164: 0 4.164 - 5.205: 2 Chirality restraints: 2876 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.77 -5.21 2.00e-01 2.50e+01 6.77e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.52 5.05 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C17 1N7 E 707 " pdb=" C16 1N7 E 707 " pdb=" C18 1N7 E 707 " pdb=" O3 1N7 E 707 " both_signs ideal model delta sigma weight residual False 2.40 2.81 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 2873 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO A 339 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 115 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO D 116 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 94 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.026 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 6783 2.89 - 3.56: 24505 3.56 - 4.23: 41139 4.23 - 4.90: 68952 Nonbonded interactions: 141396 Sorted by model distance: nonbonded pdb=" O2B ADP E 704 " pdb="MG MG E 705 " model vdw 1.546 2.170 nonbonded pdb=" PB ADP E 704 " pdb="MG MG E 705 " model vdw 1.715 2.530 nonbonded pdb=" OD2 ASP A 218 " pdb=" O2A ADP A1004 " model vdw 1.784 3.040 nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.808 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.859 2.170 ... (remaining 141391 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 'B' and resid 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.000 Extract box with map and model: 6.870 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 57.580 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.008 0.163 17884 Z= 0.540 Angle : 0.768 10.311 24672 Z= 0.394 Chirality : 0.145 5.205 2876 Planarity : 0.004 0.052 2832 Dihedral : 17.651 145.193 7224 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 7.54 % Allowed : 10.99 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.18), residues: 1953 helix: -0.86 (0.17), residues: 824 sheet: -1.70 (0.34), residues: 213 loop : -2.41 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 182 HIS 0.010 0.001 HIS E 290 PHE 0.026 0.002 PHE A 348 TYR 0.023 0.002 TYR A 788 ARG 0.005 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 192 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8629 (t0) cc_final: 0.8352 (t0) REVERT: A 164 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: A 231 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 552 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8044 (m-40) REVERT: A 576 LEU cc_start: 0.8561 (mp) cc_final: 0.8283 (mt) REVERT: A 638 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 648 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 666 MET cc_start: 0.7730 (mtt) cc_final: 0.7469 (mtt) REVERT: A 703 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: B 48 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: B 51 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7161 (ttp80) REVERT: B 100 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (t0) REVERT: B 122 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 161 ASP cc_start: 0.7416 (p0) cc_final: 0.7171 (p0) REVERT: C 5 ASP cc_start: 0.8579 (t0) cc_final: 0.8059 (t0) REVERT: D 57 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7027 (ttp-110) REVERT: E 121 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8214 (pt) REVERT: E 124 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7025 (t0) REVERT: E 263 SER cc_start: 0.8321 (p) cc_final: 0.7957 (t) REVERT: E 347 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7260 (ptpt) REVERT: E 349 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.6912 (m110) REVERT: E 376 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (pp) REVERT: E 438 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7137 (pp) outliers start: 129 outliers final: 67 residues processed: 315 average time/residue: 0.2842 time to fit residues: 136.5691 Evaluate side-chains 236 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 291 PHE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 362 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN E 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17884 Z= 0.207 Angle : 0.572 8.890 24672 Z= 0.285 Chirality : 0.040 0.336 2876 Planarity : 0.004 0.036 2832 Dihedral : 16.486 145.459 3757 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.73 % Allowed : 15.38 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1953 helix: -0.30 (0.18), residues: 818 sheet: -1.46 (0.35), residues: 207 loop : -2.20 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.015 0.001 PHE A 348 TYR 0.028 0.001 TYR E 476 ARG 0.005 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 155 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8155 (mtpp) REVERT: A 154 ASP cc_start: 0.8523 (t0) cc_final: 0.8294 (t0) REVERT: A 164 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 231 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 348 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: A 349 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7282 (mtp85) REVERT: A 552 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: A 576 LEU cc_start: 0.8491 (mp) cc_final: 0.8135 (mt) REVERT: A 638 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 648 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 666 MET cc_start: 0.7896 (mtt) cc_final: 0.7653 (mtt) REVERT: A 703 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7899 (m-40) REVERT: A 733 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.6747 (mmt90) REVERT: B 48 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6728 (mm-30) REVERT: B 51 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7273 (ttp80) REVERT: B 100 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 5 ASP cc_start: 0.8394 (t0) cc_final: 0.7871 (t0) REVERT: D 57 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7016 (ttp-110) REVERT: D 87 MET cc_start: 0.7833 (mmt) cc_final: 0.7576 (mmt) REVERT: E 121 ILE cc_start: 0.8371 (pt) cc_final: 0.8123 (pt) REVERT: E 236 SER cc_start: 0.8767 (p) cc_final: 0.8461 (t) REVERT: E 263 SER cc_start: 0.8341 (p) cc_final: 0.7987 (t) REVERT: E 347 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7143 (ptpt) REVERT: E 349 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.6871 (m110) REVERT: E 376 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7384 (pp) outliers start: 98 outliers final: 53 residues processed: 242 average time/residue: 0.2861 time to fit residues: 105.9830 Evaluate side-chains 211 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 144 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 0.0000 chunk 182 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN E 243 GLN E 245 HIS E 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17884 Z= 0.198 Angle : 0.535 8.341 24672 Z= 0.268 Chirality : 0.039 0.251 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.746 158.940 3707 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.32 % Allowed : 15.91 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1953 helix: -0.08 (0.18), residues: 818 sheet: -1.34 (0.35), residues: 214 loop : -2.08 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 182 HIS 0.007 0.001 HIS E 290 PHE 0.014 0.001 PHE A 741 TYR 0.024 0.001 TYR E 476 ARG 0.005 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 158 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8160 (mtpp) REVERT: A 69 TYR cc_start: 0.8266 (m-80) cc_final: 0.8011 (m-80) REVERT: A 144 GLU cc_start: 0.7017 (tt0) cc_final: 0.6762 (tt0) REVERT: A 154 ASP cc_start: 0.8517 (t0) cc_final: 0.8279 (t0) REVERT: A 164 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 231 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8904 (p) REVERT: A 348 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: A 349 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: A 552 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: A 576 LEU cc_start: 0.8428 (mp) cc_final: 0.8031 (mt) REVERT: A 638 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 648 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 666 MET cc_start: 0.7617 (mtt) cc_final: 0.7367 (mtt) REVERT: A 733 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6686 (mmt90) REVERT: A 911 ASN cc_start: 0.8078 (t0) cc_final: 0.7296 (t0) REVERT: B 48 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: B 51 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7021 (ttp80) REVERT: B 100 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7885 (t0) REVERT: C 5 ASP cc_start: 0.8371 (t0) cc_final: 0.7838 (t0) REVERT: D 57 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7012 (ttp-110) REVERT: E 121 ILE cc_start: 0.8362 (pt) cc_final: 0.8115 (pt) REVERT: E 236 SER cc_start: 0.8778 (p) cc_final: 0.8491 (t) REVERT: E 263 SER cc_start: 0.8324 (p) cc_final: 0.7974 (t) REVERT: E 295 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6447 (tt) REVERT: E 347 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7317 (ptpp) REVERT: E 349 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.6828 (m110) REVERT: E 376 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7466 (pp) REVERT: E 414 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7697 (tmtt) outliers start: 91 outliers final: 51 residues processed: 238 average time/residue: 0.2818 time to fit residues: 102.5391 Evaluate side-chains 213 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 790 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17884 Z= 0.268 Angle : 0.557 8.781 24672 Z= 0.279 Chirality : 0.040 0.252 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.524 173.161 3690 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.14 % Allowed : 16.78 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1953 helix: 0.01 (0.18), residues: 821 sheet: -1.34 (0.36), residues: 194 loop : -2.07 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.006 0.001 HIS E 290 PHE 0.023 0.002 PHE A 340 TYR 0.016 0.001 TYR A 903 ARG 0.006 0.000 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 156 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8162 (mtpp) REVERT: A 69 TYR cc_start: 0.8272 (m-80) cc_final: 0.8014 (m-80) REVERT: A 144 GLU cc_start: 0.7190 (tt0) cc_final: 0.6963 (tt0) REVERT: A 154 ASP cc_start: 0.8549 (t0) cc_final: 0.8297 (t0) REVERT: A 164 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: A 231 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 348 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: A 552 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: A 576 LEU cc_start: 0.8445 (mp) cc_final: 0.8103 (mt) REVERT: A 638 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 648 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 666 MET cc_start: 0.7632 (mtt) cc_final: 0.7414 (mtt) REVERT: A 733 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6697 (mmt90) REVERT: A 911 ASN cc_start: 0.8069 (t0) cc_final: 0.7281 (t0) REVERT: B 48 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: B 51 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7104 (ttp80) REVERT: B 100 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7810 (t0) REVERT: C 5 ASP cc_start: 0.8412 (t0) cc_final: 0.7889 (t0) REVERT: D 57 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7072 (ttp-110) REVERT: D 78 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8055 (t0) REVERT: E 121 ILE cc_start: 0.8401 (pt) cc_final: 0.8160 (pt) REVERT: E 236 SER cc_start: 0.8794 (p) cc_final: 0.8472 (t) REVERT: E 295 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6468 (tt) REVERT: E 347 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7281 (ptpp) REVERT: E 349 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.6907 (m110) REVERT: E 376 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7368 (pp) REVERT: E 414 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7697 (tmtt) outliers start: 105 outliers final: 66 residues processed: 247 average time/residue: 0.2887 time to fit residues: 109.3796 Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 136 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17884 Z= 0.251 Angle : 0.553 10.787 24672 Z= 0.277 Chirality : 0.040 0.245 2876 Planarity : 0.003 0.035 2832 Dihedral : 15.393 168.416 3688 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.85 % Allowed : 18.19 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1953 helix: 0.07 (0.18), residues: 828 sheet: -1.29 (0.36), residues: 194 loop : -2.06 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.006 0.001 HIS E 290 PHE 0.016 0.001 PHE A 741 TYR 0.034 0.001 TYR E 476 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 143 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8175 (mtpp) REVERT: A 69 TYR cc_start: 0.8256 (m-80) cc_final: 0.7961 (m-80) REVERT: A 136 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: A 154 ASP cc_start: 0.8551 (t0) cc_final: 0.8315 (t0) REVERT: A 164 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: A 231 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 348 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: A 552 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: A 576 LEU cc_start: 0.8426 (mp) cc_final: 0.8023 (mt) REVERT: A 638 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 666 MET cc_start: 0.7655 (mtt) cc_final: 0.7402 (mtt) REVERT: A 703 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7889 (t0) REVERT: A 733 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6676 (mmt90) REVERT: A 911 ASN cc_start: 0.8043 (t0) cc_final: 0.7243 (t0) REVERT: B 48 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: B 51 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7142 (ttp80) REVERT: B 100 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7793 (t0) REVERT: C 5 ASP cc_start: 0.8369 (t0) cc_final: 0.7870 (t0) REVERT: D 57 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7104 (ttp-110) REVERT: D 78 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8087 (t0) REVERT: D 95 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8766 (mp) REVERT: E 121 ILE cc_start: 0.8399 (pt) cc_final: 0.8161 (pt) REVERT: E 236 SER cc_start: 0.8804 (p) cc_final: 0.8464 (t) REVERT: E 295 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6478 (tt) REVERT: E 347 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7196 (ptpp) REVERT: E 349 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7215 (m110) REVERT: E 414 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7698 (tmtt) outliers start: 100 outliers final: 70 residues processed: 231 average time/residue: 0.2861 time to fit residues: 101.8548 Evaluate side-chains 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 135 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 291 PHE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 161 optimal weight: 0.0270 chunk 90 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17884 Z= 0.155 Angle : 0.521 12.102 24672 Z= 0.257 Chirality : 0.038 0.216 2876 Planarity : 0.003 0.040 2832 Dihedral : 15.121 176.818 3683 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.15 % Allowed : 18.89 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1953 helix: 0.35 (0.19), residues: 823 sheet: -1.08 (0.37), residues: 189 loop : -1.89 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.019 0.001 PHE A 812 TYR 0.019 0.001 TYR E 476 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 151 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8145 (mtpp) REVERT: A 69 TYR cc_start: 0.8203 (m-80) cc_final: 0.7979 (m-80) REVERT: A 81 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: A 136 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: A 154 ASP cc_start: 0.8513 (t0) cc_final: 0.8278 (t0) REVERT: A 164 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: A 231 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 552 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8011 (m-40) REVERT: A 576 LEU cc_start: 0.8292 (mp) cc_final: 0.7853 (mt) REVERT: A 638 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8300 (mt) REVERT: A 666 MET cc_start: 0.7530 (mtt) cc_final: 0.7281 (mtt) REVERT: A 756 MET cc_start: 0.7003 (ttt) cc_final: 0.6788 (ttt) REVERT: A 883 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (tp) REVERT: A 911 ASN cc_start: 0.8044 (t0) cc_final: 0.7239 (t0) REVERT: B 100 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7559 (t0) REVERT: C 5 ASP cc_start: 0.8190 (t0) cc_final: 0.7735 (t0) REVERT: D 57 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7169 (ttp-110) REVERT: D 78 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8113 (t0) REVERT: D 95 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8655 (mp) REVERT: E 121 ILE cc_start: 0.8388 (pt) cc_final: 0.8137 (pt) REVERT: E 236 SER cc_start: 0.8745 (p) cc_final: 0.8405 (t) REVERT: E 295 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6489 (tt) REVERT: E 347 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7038 (ptpp) REVERT: E 349 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7231 (m110) REVERT: E 414 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7694 (tmtt) REVERT: E 436 MET cc_start: 0.7823 (mpp) cc_final: 0.7520 (mtm) outliers start: 88 outliers final: 57 residues processed: 229 average time/residue: 0.2728 time to fit residues: 96.2186 Evaluate side-chains 211 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 141 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 17884 Z= 0.527 Angle : 0.678 11.218 24672 Z= 0.343 Chirality : 0.046 0.290 2876 Planarity : 0.004 0.058 2832 Dihedral : 15.189 177.947 3667 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 6.08 % Allowed : 19.06 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1953 helix: -0.13 (0.18), residues: 833 sheet: -1.26 (0.35), residues: 204 loop : -2.18 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 916 HIS 0.010 0.001 HIS E 290 PHE 0.027 0.003 PHE E 291 TYR 0.027 0.002 TYR A 788 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 149 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8164 (mtpp) REVERT: A 69 TYR cc_start: 0.8357 (m-80) cc_final: 0.8001 (m-80) REVERT: A 81 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: A 105 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7755 (tpp-160) REVERT: A 136 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: A 154 ASP cc_start: 0.8575 (t0) cc_final: 0.8334 (t0) REVERT: A 164 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: A 231 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8895 (p) REVERT: A 348 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: A 576 LEU cc_start: 0.8577 (mp) cc_final: 0.8200 (mt) REVERT: A 638 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 666 MET cc_start: 0.7761 (mtt) cc_final: 0.7510 (mtt) REVERT: A 703 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: A 733 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6800 (mmt90) REVERT: A 756 MET cc_start: 0.7315 (ttt) cc_final: 0.7064 (ttt) REVERT: A 911 ASN cc_start: 0.8046 (t0) cc_final: 0.7242 (t0) REVERT: B 100 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 112 ASP cc_start: 0.7467 (t0) cc_final: 0.7215 (t0) REVERT: C 5 ASP cc_start: 0.8426 (t0) cc_final: 0.8008 (t0) REVERT: D 57 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7118 (ttp-110) REVERT: E 121 ILE cc_start: 0.8448 (pt) cc_final: 0.8184 (pt) REVERT: E 295 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6697 (tt) REVERT: E 347 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7214 (ptpp) REVERT: E 349 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7294 (m110) REVERT: E 414 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7647 (tptp) REVERT: E 465 LYS cc_start: 0.4087 (OUTLIER) cc_final: 0.3371 (mptt) outliers start: 104 outliers final: 72 residues processed: 241 average time/residue: 0.2878 time to fit residues: 105.9295 Evaluate side-chains 229 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 144 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 0.0770 chunk 176 optimal weight: 0.0060 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17884 Z= 0.145 Angle : 0.524 10.791 24672 Z= 0.260 Chirality : 0.038 0.202 2876 Planarity : 0.003 0.049 2832 Dihedral : 14.944 168.808 3667 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.98 % Allowed : 20.99 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1953 helix: 0.32 (0.19), residues: 817 sheet: -1.21 (0.36), residues: 201 loop : -1.85 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.018 0.001 PHE E 499 TYR 0.016 0.001 TYR E 31 ARG 0.010 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 155 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8153 (mtpp) REVERT: A 154 ASP cc_start: 0.8512 (t0) cc_final: 0.8267 (t0) REVERT: A 164 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: A 231 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 552 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7959 (m-40) REVERT: A 576 LEU cc_start: 0.8308 (mp) cc_final: 0.7864 (mt) REVERT: A 638 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 666 MET cc_start: 0.7603 (mtt) cc_final: 0.7344 (mtt) REVERT: A 756 MET cc_start: 0.7090 (ttt) cc_final: 0.6882 (ttt) REVERT: A 883 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 911 ASN cc_start: 0.8033 (t0) cc_final: 0.7255 (t0) REVERT: B 100 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7550 (t0) REVERT: D 57 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7177 (ttp-110) REVERT: E 121 ILE cc_start: 0.8419 (pt) cc_final: 0.8158 (pt) REVERT: E 295 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6637 (tt) REVERT: E 347 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7000 (ptpp) REVERT: E 349 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7407 (m110) REVERT: E 414 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7679 (tmtt) REVERT: E 436 MET cc_start: 0.7858 (mpp) cc_final: 0.7526 (mtm) outliers start: 68 outliers final: 53 residues processed: 219 average time/residue: 0.3248 time to fit residues: 109.6550 Evaluate side-chains 205 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 143 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17884 Z= 0.435 Angle : 0.637 11.131 24672 Z= 0.321 Chirality : 0.044 0.281 2876 Planarity : 0.004 0.056 2832 Dihedral : 14.975 164.608 3666 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.68 % Allowed : 20.88 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1953 helix: -0.02 (0.18), residues: 832 sheet: -1.31 (0.35), residues: 202 loop : -2.07 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.009 0.001 HIS E 290 PHE 0.022 0.002 PHE E 291 TYR 0.031 0.002 TYR A 69 ARG 0.014 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 144 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8122 (mtpp) REVERT: A 136 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: A 154 ASP cc_start: 0.8575 (t0) cc_final: 0.8335 (t0) REVERT: A 164 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: A 231 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8913 (p) REVERT: A 258 ASP cc_start: 0.7706 (t0) cc_final: 0.7409 (t0) REVERT: A 552 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7943 (m-40) REVERT: A 576 LEU cc_start: 0.8535 (mp) cc_final: 0.8163 (mt) REVERT: A 638 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8518 (mt) REVERT: A 666 MET cc_start: 0.7786 (mtt) cc_final: 0.7523 (mtt) REVERT: A 703 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8116 (t0) REVERT: A 733 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6745 (mmt90) REVERT: A 756 MET cc_start: 0.7252 (ttt) cc_final: 0.7027 (ttt) REVERT: A 902 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7825 (ttp) REVERT: A 911 ASN cc_start: 0.8037 (t0) cc_final: 0.7233 (t0) REVERT: B 100 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7774 (t0) REVERT: C 5 ASP cc_start: 0.8367 (t0) cc_final: 0.8118 (t0) REVERT: D 57 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7140 (ttp-110) REVERT: E 121 ILE cc_start: 0.8463 (pt) cc_final: 0.8191 (pt) REVERT: E 295 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6645 (tt) REVERT: E 297 LEU cc_start: 0.8150 (tt) cc_final: 0.7475 (tt) REVERT: E 347 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7066 (ptpp) REVERT: E 349 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7421 (m110) REVERT: E 414 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7595 (tptp) REVERT: E 465 LYS cc_start: 0.3954 (OUTLIER) cc_final: 0.3272 (mptt) outliers start: 80 outliers final: 63 residues processed: 218 average time/residue: 0.3001 time to fit residues: 99.2569 Evaluate side-chains 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 144 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17884 Z= 0.188 Angle : 0.546 10.935 24672 Z= 0.272 Chirality : 0.039 0.228 2876 Planarity : 0.003 0.051 2832 Dihedral : 14.833 156.443 3666 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.15 % Allowed : 21.29 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1953 helix: 0.26 (0.19), residues: 823 sheet: -1.29 (0.35), residues: 203 loop : -1.90 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.006 0.001 HIS E 290 PHE 0.019 0.001 PHE E 499 TYR 0.015 0.001 TYR E 31 ARG 0.011 0.000 ARG D 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 145 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8158 (mtpp) REVERT: A 136 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: A 154 ASP cc_start: 0.8537 (t0) cc_final: 0.8310 (t0) REVERT: A 164 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 231 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 258 ASP cc_start: 0.7748 (t0) cc_final: 0.7414 (t0) REVERT: A 552 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7879 (m-40) REVERT: A 555 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.6248 (mtm-85) REVERT: A 576 LEU cc_start: 0.8346 (mp) cc_final: 0.7903 (mt) REVERT: A 638 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 666 MET cc_start: 0.7654 (mtt) cc_final: 0.7388 (mtt) REVERT: A 756 MET cc_start: 0.7153 (ttt) cc_final: 0.6953 (ttt) REVERT: A 911 ASN cc_start: 0.8035 (t0) cc_final: 0.7270 (t0) REVERT: B 100 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7593 (t0) REVERT: C 5 ASP cc_start: 0.8321 (t0) cc_final: 0.8120 (t0) REVERT: D 57 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7165 (ttp-110) REVERT: E 121 ILE cc_start: 0.8457 (pt) cc_final: 0.8179 (pt) REVERT: E 295 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6630 (tt) REVERT: E 297 LEU cc_start: 0.8113 (tt) cc_final: 0.7347 (tt) REVERT: E 347 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7060 (ptpp) REVERT: E 349 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7355 (m110) REVERT: E 414 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7642 (tptp) REVERT: E 436 MET cc_start: 0.7867 (mpp) cc_final: 0.7549 (mtm) REVERT: E 465 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3261 (mptt) outliers start: 71 outliers final: 56 residues processed: 210 average time/residue: 0.3120 time to fit residues: 98.8420 Evaluate side-chains 211 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 145 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 7.9990 chunk 48 optimal weight: 0.0000 chunk 147 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 140 optimal weight: 8.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS D 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110914 restraints weight = 20082.559| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.20 r_work: 0.2948 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17884 Z= 0.144 Angle : 0.511 10.900 24672 Z= 0.253 Chirality : 0.038 0.202 2876 Planarity : 0.003 0.052 2832 Dihedral : 14.528 138.070 3666 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.57 % Allowed : 21.99 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1953 helix: 0.54 (0.19), residues: 810 sheet: -1.13 (0.36), residues: 203 loop : -1.81 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 182 HIS 0.004 0.001 HIS A 309 PHE 0.020 0.001 PHE E 499 TYR 0.013 0.001 TYR E 476 ARG 0.008 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3912.14 seconds wall clock time: 72 minutes 25.74 seconds (4345.74 seconds total)