Starting phenix.real_space_refine on Fri Feb 23 02:04:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c66_7347/02_2024/6c66_7347.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 146 5.49 5 S 72 5.16 5 C 22323 2.51 5 N 6607 2.21 5 O 7105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "G ARG 504": "NH1" <-> "NH2" Residue "G ARG 505": "NH1" <-> "NH2" Residue "G ARG 528": "NH1" <-> "NH2" Residue "G ARG 692": "NH1" <-> "NH2" Residue "G ARG 784": "NH1" <-> "NH2" Residue "G ARG 847": "NH1" <-> "NH2" Residue "G ARG 867": "NH1" <-> "NH2" Residue "G ARG 917": "NH1" <-> "NH2" Residue "G ARG 932": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H ARG 172": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K ARG 211": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "M ARG 217": "NH1" <-> "NH2" Residue "O ARG 181": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36255 Number of models: 1 Model: "" Number of chains: 16 Chain: "G" Number of atoms: 6467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6467 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 56, 'TRANS': 771} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4053 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 3, 'PTRANS': 42, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2501 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 5, 'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "D" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2835 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 351} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2825 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 350} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "H" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2553 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Chain: "I" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Chain: "K" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1325 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1012 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "M" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1916 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 20, 'TRANS': 223} Chain breaks: 1 Chain: "N" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 766 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1652 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 5, 'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.53, per 1000 atoms: 0.54 Number of scatterers: 36255 At special positions: 0 Unit cell: (203.36, 169.88, 147.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 72 16.00 P 146 15.00 O 7105 8.00 N 6607 7.00 C 22323 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: 15.79 Conformation dependent library (CDL) restraints added in 6.2 seconds 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 37 sheets defined 44.9% alpha, 16.0% beta 35 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 11.13 Creating SS restraints... Processing helix chain 'G' and resid 34 through 52 Processing helix chain 'G' and resid 54 through 65 Processing helix chain 'G' and resid 68 through 83 Processing helix chain 'G' and resid 84 through 88 Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.547A pdb=" N GLN G 95 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 96 " --> pdb=" O GLN G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 96' Processing helix chain 'G' and resid 114 through 127 Proline residue: G 124 - end of helix removed outlier: 3.508A pdb=" N LEU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 131 Processing helix chain 'G' and resid 137 through 148 Processing helix chain 'G' and resid 163 through 168 Processing helix chain 'G' and resid 172 through 190 Processing helix chain 'G' and resid 200 through 220 Processing helix chain 'G' and resid 236 through 250 Processing helix chain 'G' and resid 251 through 259 removed outlier: 3.730A pdb=" N LEU G 255 " --> pdb=" O ILE G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 295 Proline residue: G 292 - end of helix Processing helix chain 'G' and resid 310 through 327 removed outlier: 3.948A pdb=" N ALA G 314 " --> pdb=" O GLY G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 348 removed outlier: 3.720A pdb=" N ASP G 342 " --> pdb=" O MET G 338 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR G 346 " --> pdb=" O ASP G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 416 Processing helix chain 'G' and resid 423 through 428 Processing helix chain 'G' and resid 429 through 431 No H-bonds generated for 'chain 'G' and resid 429 through 431' Processing helix chain 'G' and resid 435 through 445 removed outlier: 3.964A pdb=" N ARG G 439 " --> pdb=" O HIS G 435 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY G 445 " --> pdb=" O PHE G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 474 Processing helix chain 'G' and resid 486 through 503 Processing helix chain 'G' and resid 535 through 539 Processing helix chain 'G' and resid 566 through 575 removed outlier: 4.369A pdb=" N VAL G 570 " --> pdb=" O ASN G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 594 Processing helix chain 'G' and resid 595 through 602 Processing helix chain 'G' and resid 602 through 609 removed outlier: 3.508A pdb=" N THR G 608 " --> pdb=" O GLN G 604 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU G 609 " --> pdb=" O TRP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 637 Processing helix chain 'G' and resid 640 through 647 removed outlier: 3.679A pdb=" N GLY G 647 " --> pdb=" O GLY G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 659 through 664 Processing helix chain 'G' and resid 679 through 687 Processing helix chain 'G' and resid 688 through 690 No H-bonds generated for 'chain 'G' and resid 688 through 690' Processing helix chain 'G' and resid 736 through 749 removed outlier: 3.558A pdb=" N ARG G 749 " --> pdb=" O THR G 745 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 771 removed outlier: 3.787A pdb=" N TYR G 769 " --> pdb=" O VAL G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 772 through 775 Processing helix chain 'G' and resid 777 through 797 removed outlier: 3.582A pdb=" N ASN G 797 " --> pdb=" O GLY G 793 " (cutoff:3.500A) Processing helix chain 'G' and resid 810 through 814 Processing helix chain 'G' and resid 863 through 867 Processing helix chain 'G' and resid 869 through 878 Processing helix chain 'G' and resid 886 through 891 removed outlier: 4.033A pdb=" N SER G 890 " --> pdb=" O GLY G 886 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN G 891 " --> pdb=" O PRO G 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 886 through 891' Processing helix chain 'G' and resid 899 through 904 removed outlier: 3.576A pdb=" N ARG G 903 " --> pdb=" O PRO G 899 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU G 904 " --> pdb=" O GLU G 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 899 through 904' Processing helix chain 'G' and resid 905 through 910 removed outlier: 4.630A pdb=" N ASP G 910 " --> pdb=" O PHE G 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.792A pdb=" N ARG A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.589A pdb=" N GLU A 140 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.463A pdb=" N LYS A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.564A pdb=" N LEU A 341 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 343 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.841A pdb=" N ALA A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 446 removed outlier: 3.728A pdb=" N VAL A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 486 removed outlier: 4.194A pdb=" N HIS A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Proline residue: A 479 - end of helix removed outlier: 3.611A pdb=" N TYR A 486 " --> pdb=" O TRP A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 516 Processing helix chain 'A' and resid 517 through 520 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.815A pdb=" N VAL B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.588A pdb=" N GLY B 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.988A pdb=" N GLU B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 239 through 244 removed outlier: 4.279A pdb=" N GLU B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.630A pdb=" N TRP C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.513A pdb=" N GLU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 120 through 133 removed outlier: 3.580A pdb=" N ILE C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 144 removed outlier: 3.915A pdb=" N LYS C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 161 removed outlier: 3.517A pdb=" N ILE C 156 " --> pdb=" O PRO C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 355 through 367 Processing helix chain 'D' and resid 39 through 55 removed outlier: 3.771A pdb=" N TRP D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.509A pdb=" N ILE D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 164 through 171 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 249 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 355 through 368 Processing helix chain 'E' and resid 39 through 55 removed outlier: 3.737A pdb=" N TRP E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 120 through 133 Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 249 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 310 through 329 Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'F' and resid 39 through 55 removed outlier: 3.744A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 120 through 133 Processing helix chain 'F' and resid 134 through 143 removed outlier: 3.507A pdb=" N ALA F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.545A pdb=" N LYS F 161 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 249 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 310 through 329 Processing helix chain 'F' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 55 removed outlier: 3.614A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.556A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 120 through 133 removed outlier: 3.520A pdb=" N ILE H 124 " --> pdb=" O PRO H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 249 through 266 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 310 through 329 Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 6 through 24 removed outlier: 4.382A pdb=" N VAL I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 33 removed outlier: 4.007A pdb=" N ARG I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG I 33 " --> pdb=" O ALA I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 47 through 52 Processing helix chain 'I' and resid 53 through 55 No H-bonds generated for 'chain 'I' and resid 53 through 55' Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 92 through 100 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.814A pdb=" N SER I 142 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 166 removed outlier: 3.791A pdb=" N GLN I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 186 removed outlier: 3.723A pdb=" N HIS I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Proline residue: I 177 - end of helix Processing helix chain 'I' and resid 191 through 201 removed outlier: 3.600A pdb=" N LEU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 209 through 227 Processing helix chain 'K' and resid 4 through 24 removed outlier: 3.966A pdb=" N HIS K 9 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 33 Processing helix chain 'K' and resid 45 through 51 Processing helix chain 'K' and resid 52 through 55 removed outlier: 3.577A pdb=" N VAL K 55 " --> pdb=" O ALA K 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 52 through 55' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.731A pdb=" N VAL K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 97 Processing helix chain 'K' and resid 138 through 150 Processing helix chain 'K' and resid 153 through 166 removed outlier: 3.854A pdb=" N GLN K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 185 removed outlier: 3.752A pdb=" N HIS K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG K 174 " --> pdb=" O ASP K 170 " (cutoff:3.500A) Proline residue: K 177 - end of helix Processing helix chain 'K' and resid 191 through 205 removed outlier: 4.363A pdb=" N GLY K 203 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 228 removed outlier: 3.682A pdb=" N VAL K 209 " --> pdb=" O THR K 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 51 through 55 Processing helix chain 'M' and resid 95 through 99 removed outlier: 3.505A pdb=" N ALA M 99 " --> pdb=" O PRO M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 130 Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.774A pdb=" N GLU M 161 " --> pdb=" O ASP M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 231 removed outlier: 3.514A pdb=" N LEU M 230 " --> pdb=" O PRO M 227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL M 231 " --> pdb=" O ALA M 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 227 through 231' Processing helix chain 'M' and resid 236 through 248 removed outlier: 3.698A pdb=" N ASN M 240 " --> pdb=" O ARG M 236 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 removed outlier: 3.999A pdb=" N LEU O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 144 through 153 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'O' and resid 213 through 217 removed outlier: 3.914A pdb=" N GLY O 217 " --> pdb=" O LYS O 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.235A pdb=" N LYS G 23 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR G 32 " --> pdb=" O LYS G 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 421 through 422 removed outlier: 5.817A pdb=" N PHE G 332 " --> pdb=" O VAL G 449 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP G 451 " --> pdb=" O PHE G 332 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA G 334 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL G 448 " --> pdb=" O VAL G 479 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU G 481 " --> pdb=" O VAL G 448 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL G 450 " --> pdb=" O LEU G 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 617 through 618 removed outlier: 6.951A pdb=" N TYR G 617 " --> pdb=" O VAL G 657 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE G 587 " --> pdb=" O ALA G 658 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA G 586 " --> pdb=" O ILE G 674 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASP G 676 " --> pdb=" O ALA G 586 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE G 588 " --> pdb=" O ASP G 676 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N MET G 673 " --> pdb=" O VAL G 711 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU G 713 " --> pdb=" O MET G 673 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER G 675 " --> pdb=" O LEU G 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU G 552 " --> pdb=" O LEU G 710 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL G 712 " --> pdb=" O GLU G 552 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG G 554 " --> pdb=" O VAL G 712 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR G 714 " --> pdb=" O ARG G 554 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL G 556 " --> pdb=" O THR G 714 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 560 through 561 Processing sheet with id=AA5, first strand: chain 'G' and resid 833 through 836 Processing sheet with id=AA6, first strand: chain 'G' and resid 840 through 841 removed outlier: 3.509A pdb=" N VAL G 918 " --> pdb=" O VAL G 841 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 917 " --> pdb=" O LEU G 925 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 927 through 928 Processing sheet with id=AA8, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA9, first strand: chain 'A' and resid 176 through 177 removed outlier: 3.920A pdb=" N ASP A 293 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AB2, first strand: chain 'A' and resid 219 through 224 Processing sheet with id=AB3, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AB4, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 188 removed outlier: 6.238A pdb=" N SER B 227 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 14 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG B 335 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'C' and resid 186 through 188 Processing sheet with id=AB8, first strand: chain 'C' and resid 186 through 188 removed outlier: 6.367A pdb=" N SER C 227 " --> pdb=" O TYR C 14 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR C 14 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ARG C 335 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AC1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC2, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.670A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 192 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 186 through 188 removed outlier: 6.249A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG D 335 " --> pdb=" O GLU D 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 61 through 62 Processing sheet with id=AC5, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.372A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 192 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 186 through 188 removed outlier: 4.643A pdb=" N GLY E 229 " --> pdb=" O PRO E 13 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE E 231 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR E 11 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG E 233 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE E 9 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA E 235 " --> pdb=" O HIS E 7 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS E 7 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 237 " --> pdb=" O ASP E 5 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP E 5 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG E 335 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AC8, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.556A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 192 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 186 through 188 removed outlier: 4.657A pdb=" N GLY F 229 " --> pdb=" O PRO F 13 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE F 231 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR F 11 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG F 233 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 9 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA F 235 " --> pdb=" O HIS F 7 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS F 7 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 237 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP F 5 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG F 335 " --> pdb=" O GLU F 351 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 61 through 62 Processing sheet with id=AD2, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.398A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE H 192 " --> pdb=" O TYR H 232 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.398A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE H 192 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG H 335 " --> pdb=" O GLU H 351 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 61 through 62 Processing sheet with id=AD5, first strand: chain 'M' and resid 150 through 152 removed outlier: 5.499A pdb=" N VAL M 150 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG M 7 " --> pdb=" O VAL M 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 112 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR M 60 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP M 183 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ARG M 65 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 13.327A pdb=" N LEU M 181 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG M 213 " --> pdb=" O PRO M 204 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER M 215 " --> pdb=" O ASP M 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AD7, first strand: chain 'O' and resid 52 through 55 Processing sheet with id=AD8, first strand: chain 'O' and resid 188 through 195 removed outlier: 3.691A pdb=" N SER O 222 " --> pdb=" O ARG O 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 112 through 114 Processing sheet with id=AE1, first strand: chain 'O' and resid 170 through 171 1564 hydrogen bonds defined for protein. 4287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 13.96 Time building geometry restraints manager: 16.80 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: 9395 1.33 - 1.45: 7728 1.45 - 1.57: 19793 1.57 - 1.69: 287 1.69 - 1.81: 120 Bond restraints: 37323 Sorted by residual: bond pdb=" CA ASP A 356 " pdb=" C ASP A 356 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.72e-02 3.38e+03 1.35e+01 bond pdb=" C ILE F 150 " pdb=" N LEU F 151 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.83e-02 1.25e+03 1.27e+01 bond pdb=" C2' C J 46 " pdb=" C1' C J 46 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.50e-02 4.44e+03 4.18e+00 bond pdb=" N PHE G 223 " pdb=" CA PHE G 223 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.16e+00 bond pdb=" CB MET A 470 " pdb=" CG MET A 470 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.47e+00 ... (remaining 37318 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.53: 1181 104.53 - 112.18: 18907 112.18 - 119.83: 14124 119.83 - 127.48: 16488 127.48 - 135.13: 674 Bond angle restraints: 51374 Sorted by residual: angle pdb=" C ASP G 222 " pdb=" N PHE G 223 " pdb=" CA PHE G 223 " ideal model delta sigma weight residual 121.70 135.13 -13.43 1.80e+00 3.09e-01 5.57e+01 angle pdb=" C ASN O 119 " pdb=" N ASN O 120 " pdb=" CA ASN O 120 " ideal model delta sigma weight residual 121.70 133.51 -11.81 1.80e+00 3.09e-01 4.30e+01 angle pdb=" C THR O 167 " pdb=" N LEU O 168 " pdb=" CA LEU O 168 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 angle pdb=" C GLN B 89 " pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 121.97 131.63 -9.66 1.80e+00 3.09e-01 2.88e+01 angle pdb=" C TYR A 493 " pdb=" N THR A 494 " pdb=" CA THR A 494 " ideal model delta sigma weight residual 121.48 132.06 -10.58 2.04e+00 2.40e-01 2.69e+01 ... (remaining 51369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 21380 31.11 - 62.23: 796 62.23 - 93.34: 107 93.34 - 124.45: 1 124.45 - 155.57: 4 Dihedral angle restraints: 22288 sinusoidal: 9927 harmonic: 12361 Sorted by residual: dihedral pdb=" O4' C J 55 " pdb=" C1' C J 55 " pdb=" N1 C J 55 " pdb=" C2 C J 55 " ideal model delta sinusoidal sigma weight residual 200.00 54.55 145.45 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" O4' U J 20 " pdb=" C1' U J 20 " pdb=" N1 U J 20 " pdb=" C2 U J 20 " ideal model delta sinusoidal sigma weight residual 200.00 62.73 137.27 1 1.50e+01 4.44e-03 7.40e+01 dihedral pdb=" CA GLU A 346 " pdb=" C GLU A 346 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " ideal model delta harmonic sigma weight residual 0.00 -28.69 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 22285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 5537 0.117 - 0.235: 266 0.235 - 0.352: 10 0.352 - 0.469: 0 0.469 - 0.586: 1 Chirality restraints: 5814 Sorted by residual: chirality pdb=" CB VAL M 61 " pdb=" CA VAL M 61 " pdb=" CG1 VAL M 61 " pdb=" CG2 VAL M 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" CB THR D 230 " pdb=" CA THR D 230 " pdb=" OG1 THR D 230 " pdb=" CG2 THR D 230 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB THR F 230 " pdb=" CA THR F 230 " pdb=" OG1 THR F 230 " pdb=" CG2 THR F 230 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 5811 not shown) Planarity restraints: 6199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G J 19 " 0.051 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" N9 G J 19 " -0.054 2.00e-02 2.50e+03 pdb=" C8 G J 19 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G J 19 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G J 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G J 19 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G J 19 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G J 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G J 19 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G J 19 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G J 19 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G J 19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 202 " 0.025 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP I 202 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP I 202 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP I 202 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP I 202 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP I 202 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 202 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 202 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 202 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 202 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 390 " -0.032 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP A 390 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 390 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 390 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 390 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 390 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 390 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 390 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 390 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 390 " -0.004 2.00e-02 2.50e+03 ... (remaining 6196 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 190 2.43 - 3.05: 24063 3.05 - 3.66: 55651 3.66 - 4.28: 81699 4.28 - 4.90: 134200 Nonbonded interactions: 295803 Sorted by model distance: nonbonded pdb=" OD2 ASP G 84 " pdb="FE FE G1002 " model vdw 1.812 2.260 nonbonded pdb=" OP1 DA N 21 " pdb="FE FE G1001 " model vdw 1.878 2.260 nonbonded pdb=" OD1 ASP G 215 " pdb="FE FE G1002 " model vdw 1.924 2.260 nonbonded pdb=" OD1 ASP G 84 " pdb="FE FE G1001 " model vdw 2.018 2.260 nonbonded pdb=" OP2 DA N 21 " pdb="FE FE G1002 " model vdw 2.049 2.260 ... (remaining 295798 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 2 through 198 or resid 227 through 235 or (resid 236 and ( \ name N or name CA or name C or name O or name CB )) or resid 237 through 269 or \ resid 279 through 367)) selection = (chain 'C' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 68 or (resi \ d 69 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 74 or (resid 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 81 and (name N or name CA or n \ ame C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 92 or resid 117 t \ hrough 118 or (resid 119 and (name N or name CA or name C or name O or name CB ) \ ) or resid 120 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 126 or (resid 127 through 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 134 or (resid 135 through 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 140 or (resid 150 through 151 and (name N or name \ CA or name C or name O or name CB )) or resid 152 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 175 or (resid 176 through 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 through 198 or resid 227 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 and (name N or name CA or name C or name O or name \ CB )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 through 269 or resid 279 through \ 367)) selection = (chain 'D' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 68 or (resi \ d 69 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 74 or (resid 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 81 and (name N or name CA or n \ ame C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 92 or resid 117 t \ hrough 118 or (resid 119 and (name N or name CA or name C or name O or name CB ) \ ) or resid 120 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 126 or (resid 127 through 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 134 or (resid 135 through 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 140 or (resid 150 through 151 and (name N or name \ CA or name C or name O or name CB )) or resid 152 through 162 or (resid 163 thr \ ough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 t \ hrough 175 or (resid 176 through 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 198 or resid 227 through 232 or (resid 233 an \ d (name N or name CA or name C or name O or name CB )) or resid 234 through 239 \ or (resid 240 through 241 and (name N or name CA or name C or name O or name CB \ )) or resid 242 through 269 or resid 279 through 367)) selection = (chain 'E' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 68 or (resi \ d 69 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 74 or (resid 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 81 and (name N or name CA or n \ ame C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 92 or resid 117 t \ hrough 118 or (resid 119 and (name N or name CA or name C or name O or name CB ) \ ) or resid 120 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 126 or (resid 127 through 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 134 or (resid 135 through 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 140 or (resid 150 through 151 and (name N or name \ CA or name C or name O or name CB )) or resid 152 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 175 or (resid 176 through 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 through 198 or resid 227 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 and (name N or name CA or name C or name O or name \ CB )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 through 269 or resid 279 through \ 367)) selection = (chain 'F' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 68 or (resi \ d 69 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 74 or (resid 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 81 and (name N or name CA or n \ ame C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 92 or resid 117 t \ hrough 118 or (resid 119 and (name N or name CA or name C or name O or name CB ) \ ) or resid 120 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 126 or (resid 127 through 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 134 or (resid 135 through 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 140 or (resid 150 through 151 and (name N or name \ CA or name C or name O or name CB )) or resid 152 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 175 or (resid 176 through 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 through 198 or resid 227 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 and (name N or name CA or name C or name O or name \ CB )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 through 269 or resid 279 through \ 367)) selection = (chain 'H' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 68 or (resi \ d 69 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 74 or (resid 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 81 and (name N or name CA or n \ ame C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 92 or resid 117 t \ hrough 118 or (resid 119 and (name N or name CA or name C or name O or name CB ) \ ) or resid 120 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 126 or (resid 127 through 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 134 or (resid 135 through 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 140 or (resid 150 through 151 and (name N or name \ CA or name C or name O or name CB )) or resid 152 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 175 or (resid 176 through 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 through 232 or (resid 233 and (name N \ or name CA or name C or name O or name CB )) or resid 234 through 235 or (resid \ 236 and (name N or name CA or name C or name O or name CB )) or resid 237 throu \ gh 239 or (resid 240 through 241 and (name N or name CA or name C or name O or n \ ame CB )) or resid 242 through 367)) } ncs_group { reference = (chain 'I' and (resid 5 through 35 or resid 44 through 57 or resid 75 through 98 \ or resid 136 through 229)) selection = (chain 'K' and (resid 5 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 229)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.030 Extract box with map and model: 5.940 Check model and map are aligned: 0.520 Set scattering table: 0.360 Process input model: 101.500 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.150 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 0.102 37323 Z= 0.499 Angle : 1.110 13.964 51374 Z= 0.629 Chirality : 0.057 0.586 5814 Planarity : 0.007 0.080 6199 Dihedral : 15.127 155.568 14288 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.13 % Favored : 91.70 % Rotamer: Outliers : 1.55 % Allowed : 1.02 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.10), residues: 4206 helix: -3.06 (0.09), residues: 1691 sheet: -2.36 (0.18), residues: 552 loop : -3.21 (0.11), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP I 202 HIS 0.012 0.002 HIS G 620 PHE 0.032 0.003 PHE A 379 TYR 0.040 0.003 TYR K 82 ARG 0.023 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 694 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 ARG cc_start: 0.5918 (mpp80) cc_final: 0.4889 (ttp80) REVERT: G 465 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: G 510 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5589 (mm-30) REVERT: G 717 GLN cc_start: 0.4067 (tt0) cc_final: 0.2723 (mm-40) REVERT: G 852 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6214 (pt0) REVERT: G 870 MET cc_start: 0.5321 (mmt) cc_final: 0.4765 (tpt) REVERT: G 885 MET cc_start: 0.3149 (tpp) cc_final: 0.2914 (tpp) REVERT: A 167 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8177 (m90) REVERT: A 235 ASN cc_start: 0.8405 (m110) cc_final: 0.8013 (m110) REVERT: A 308 GLU cc_start: 0.7869 (tp30) cc_final: 0.7545 (tp30) REVERT: B 48 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8835 (ttm-80) REVERT: B 61 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.3935 (tpp80) REVERT: B 140 LYS cc_start: 0.4553 (mmtm) cc_final: 0.4041 (tptp) REVERT: B 155 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4489 (ptp90) REVERT: B 202 ASP cc_start: 0.8546 (t0) cc_final: 0.8305 (t0) REVERT: B 212 LYS cc_start: 0.8542 (pttt) cc_final: 0.8153 (pttp) REVERT: B 286 ILE cc_start: 0.9488 (mp) cc_final: 0.9276 (mt) REVERT: B 361 ASP cc_start: 0.8426 (m-30) cc_final: 0.8137 (m-30) REVERT: C 173 MET cc_start: 0.8593 (ttm) cc_final: 0.8220 (ttp) REVERT: C 236 ASN cc_start: 0.8300 (m-40) cc_final: 0.7450 (m-40) REVERT: D 20 ASP cc_start: 0.7996 (t0) cc_final: 0.7784 (p0) REVERT: D 317 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8194 (tm-30) REVERT: E 20 ASP cc_start: 0.8198 (t0) cc_final: 0.7957 (t0) REVERT: E 106 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7174 (mttt) REVERT: E 118 TYR cc_start: 0.8679 (t80) cc_final: 0.8375 (t80) REVERT: F 148 LYS cc_start: 0.8739 (ptpt) cc_final: 0.8084 (mttm) REVERT: F 154 ASP cc_start: 0.8521 (t0) cc_final: 0.8184 (t0) REVERT: F 187 GLN cc_start: 0.8909 (mt0) cc_final: 0.8690 (mt0) REVERT: F 308 ASP cc_start: 0.8164 (m-30) cc_final: 0.7867 (m-30) REVERT: I 23 ASN cc_start: 0.8451 (t0) cc_final: 0.8146 (t0) REVERT: I 88 MET cc_start: 0.8872 (mtm) cc_final: 0.8645 (mtp) REVERT: I 196 ILE cc_start: 0.8722 (pt) cc_final: 0.8326 (mt) REVERT: I 205 THR cc_start: 0.5605 (t) cc_final: 0.5323 (t) REVERT: K 78 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6510 (tm-30) REVERT: K 191 ASP cc_start: 0.7093 (m-30) cc_final: 0.6785 (m-30) REVERT: K 222 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tm-30) REVERT: M 104 SER cc_start: 0.9325 (t) cc_final: 0.9009 (p) REVERT: M 172 ARG cc_start: 0.5978 (mmt180) cc_final: 0.5678 (mmp-170) REVERT: O 5 THR cc_start: 0.0422 (t) cc_final: -0.0127 (t) outliers start: 53 outliers final: 26 residues processed: 744 average time/residue: 0.5585 time to fit residues: 638.5188 Evaluate side-chains 366 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 333 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain G residue 470 TRP Chi-restraints excluded: chain G residue 504 ARG Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain O residue 61 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 221 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 394 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 220 GLN G 290 HIS G 664 GLN G 685 GLN G 695 HIS A 95 GLN A 160 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 283 HIS A 363 GLN A 445 ASN A 532 HIS B 7 HIS B 10 GLN B 168 ASN B 187 GLN B 195 HIS B 214 ASN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS C 49 HIS C 195 HIS C 220 HIS C 236 ASN C 272 GLN D 7 HIS D 49 HIS D 195 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS E 49 HIS E 134 HIS E 195 HIS ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 HIS F 49 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS F 285 HIS H 7 HIS H 49 HIS H 134 HIS H 195 HIS H 285 HIS I 8 GLN I 173 HIS I 208 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS M 13 GLN M 201 ASN ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37323 Z= 0.202 Angle : 0.741 13.193 51374 Z= 0.379 Chirality : 0.043 0.298 5814 Planarity : 0.006 0.069 6199 Dihedral : 17.316 151.861 6665 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.18 % Favored : 93.58 % Rotamer: Outliers : 2.45 % Allowed : 10.45 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.74 (0.11), residues: 4206 helix: -1.11 (0.11), residues: 1754 sheet: -1.67 (0.19), residues: 569 loop : -2.52 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 148 HIS 0.016 0.001 HIS B 220 PHE 0.020 0.002 PHE A 379 TYR 0.025 0.002 TYR G 316 ARG 0.008 0.001 ARG F 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 441 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.4025 (tt0) cc_final: 0.2613 (mm-40) REVERT: G 837 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4700 (mt) REVERT: G 870 MET cc_start: 0.5103 (mmt) cc_final: 0.4648 (tpt) REVERT: G 906 PHE cc_start: 0.5637 (p90) cc_final: 0.3880 (t80) REVERT: G 937 ASP cc_start: 0.4901 (t70) cc_final: 0.3916 (p0) REVERT: A 235 ASN cc_start: 0.8020 (m110) cc_final: 0.7751 (m110) REVERT: A 308 GLU cc_start: 0.7738 (tp30) cc_final: 0.7521 (tp30) REVERT: B 43 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6447 (m100) REVERT: B 61 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.3920 (mmt-90) REVERT: B 172 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7742 (ppt170) REVERT: B 317 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6816 (tm-30) REVERT: D 173 MET cc_start: 0.8719 (ttt) cc_final: 0.8257 (ttt) REVERT: D 317 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7742 (tm-30) REVERT: E 20 ASP cc_start: 0.8083 (t0) cc_final: 0.7854 (t0) REVERT: E 82 LEU cc_start: 0.8459 (mm) cc_final: 0.8198 (tp) REVERT: F 148 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8032 (mttm) REVERT: F 363 MET cc_start: 0.9093 (mmt) cc_final: 0.8754 (mmp) REVERT: H 41 GLN cc_start: 0.8876 (pm20) cc_final: 0.8471 (pm20) REVERT: H 97 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7675 (ptpp) REVERT: I 23 ASN cc_start: 0.8322 (t0) cc_final: 0.8039 (t0) REVERT: I 88 MET cc_start: 0.8837 (mtm) cc_final: 0.8575 (mtp) REVERT: I 196 ILE cc_start: 0.8922 (pt) cc_final: 0.8310 (mt) REVERT: I 212 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: K 78 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6512 (tm-30) REVERT: K 82 TYR cc_start: 0.5887 (p90) cc_final: 0.5235 (p90) REVERT: K 88 MET cc_start: 0.9141 (tpp) cc_final: 0.8818 (tpp) REVERT: K 187 GLN cc_start: 0.8876 (mp10) cc_final: 0.8326 (mp10) REVERT: K 222 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7225 (tm-30) REVERT: M 17 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6717 (tm-30) REVERT: O 62 LEU cc_start: 0.2705 (mt) cc_final: 0.2474 (mt) outliers start: 84 outliers final: 48 residues processed: 498 average time/residue: 0.5219 time to fit residues: 413.8393 Evaluate side-chains 348 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 295 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 504 ARG Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 170 ASP Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 394 optimal weight: 5.9990 chunk 426 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 391 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 HIS G 184 HIS G 435 HIS G 581 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 349 ASN A 505 ASN B 245 ASN B 285 HIS C 236 ASN C 272 GLN D 134 HIS D 187 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS I 167 GLN ** I 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS M 239 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 37323 Z= 0.406 Angle : 0.780 12.526 51374 Z= 0.405 Chirality : 0.046 0.274 5814 Planarity : 0.006 0.076 6199 Dihedral : 17.239 152.966 6619 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.01 % Favored : 92.82 % Rotamer: Outliers : 3.97 % Allowed : 13.57 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.07 (0.12), residues: 4206 helix: -0.51 (0.12), residues: 1765 sheet: -1.31 (0.19), residues: 565 loop : -2.21 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 43 HIS 0.010 0.002 HIS D 195 PHE 0.023 0.002 PHE E 204 TYR 0.030 0.002 TYR K 82 ARG 0.013 0.001 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 308 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 497 TYR cc_start: 0.7360 (t80) cc_final: 0.7145 (t80) REVERT: G 717 GLN cc_start: 0.4309 (tt0) cc_final: 0.2824 (mm-40) REVERT: G 870 MET cc_start: 0.5135 (mmt) cc_final: 0.4495 (mmt) REVERT: G 937 ASP cc_start: 0.4856 (t70) cc_final: 0.3818 (p0) REVERT: A 235 ASN cc_start: 0.8329 (m110) cc_final: 0.8043 (m110) REVERT: A 308 GLU cc_start: 0.7907 (tp30) cc_final: 0.7623 (tp30) REVERT: B 61 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.3696 (mmp-170) REVERT: B 172 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7755 (ppt170) REVERT: B 250 GLN cc_start: 0.8277 (pp30) cc_final: 0.7802 (pp30) REVERT: C 221 MET cc_start: 0.8653 (mtp) cc_final: 0.8107 (ptp) REVERT: D 173 MET cc_start: 0.9334 (ttt) cc_final: 0.8239 (ttt) REVERT: D 317 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 20 ASP cc_start: 0.8300 (t0) cc_final: 0.8074 (t0) REVERT: E 214 ASN cc_start: 0.7958 (t0) cc_final: 0.7727 (t0) REVERT: F 43 TRP cc_start: 0.8704 (OUTLIER) cc_final: 0.8417 (t60) REVERT: F 148 LYS cc_start: 0.8739 (ptpt) cc_final: 0.8304 (mmtt) REVERT: H 97 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7662 (ptpp) REVERT: H 286 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8805 (mp) REVERT: I 23 ASN cc_start: 0.8340 (t0) cc_final: 0.8033 (t0) REVERT: I 88 MET cc_start: 0.8969 (mtm) cc_final: 0.8689 (mtp) REVERT: I 207 ARG cc_start: 0.7303 (ppt170) cc_final: 0.6739 (pmt-80) REVERT: K 78 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6678 (tm-30) REVERT: K 186 ASP cc_start: 0.7938 (m-30) cc_final: 0.7667 (m-30) REVERT: K 187 GLN cc_start: 0.8884 (mp10) cc_final: 0.8335 (mp10) REVERT: M 35 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8230 (pp) REVERT: M 238 TYR cc_start: 0.8832 (t80) cc_final: 0.8385 (t80) REVERT: O 62 LEU cc_start: 0.2458 (mt) cc_final: 0.2192 (mt) REVERT: O 86 MET cc_start: 0.2477 (mmt) cc_final: 0.2238 (mmt) outliers start: 136 outliers final: 85 residues processed: 408 average time/residue: 0.4648 time to fit residues: 316.4031 Evaluate side-chains 348 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 258 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 504 ARG Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 683 LEU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 189 HIS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain O residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 396 optimal weight: 1.9990 chunk 419 optimal weight: 0.0170 chunk 207 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN A 174 HIS A 349 ASN B 245 ASN C 236 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 HIS K 175 HIS O 25 ASN O 27 HIS O 150 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37323 Z= 0.201 Angle : 0.668 11.669 51374 Z= 0.342 Chirality : 0.042 0.342 5814 Planarity : 0.005 0.055 6199 Dihedral : 17.097 150.265 6610 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 3.82 % Allowed : 15.53 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.57 (0.12), residues: 4206 helix: -0.11 (0.12), residues: 1774 sheet: -1.00 (0.20), residues: 557 loop : -1.96 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP O 148 HIS 0.014 0.001 HIS O 150 PHE 0.016 0.001 PHE M 73 TYR 0.021 0.001 TYR K 82 ARG 0.006 0.000 ARG O 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 332 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.3927 (tt0) cc_final: 0.2510 (mm-40) REVERT: G 782 MET cc_start: 0.7873 (mtt) cc_final: 0.7536 (mmm) REVERT: G 870 MET cc_start: 0.5256 (mmt) cc_final: 0.4651 (mmt) REVERT: G 906 PHE cc_start: 0.5814 (p90) cc_final: 0.3864 (t80) REVERT: G 937 ASP cc_start: 0.4953 (t70) cc_final: 0.3842 (p0) REVERT: A 133 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 235 ASN cc_start: 0.8235 (m110) cc_final: 0.7916 (m110) REVERT: A 239 PRO cc_start: 0.8835 (Cg_endo) cc_final: 0.8593 (Cg_exo) REVERT: A 308 GLU cc_start: 0.7855 (tp30) cc_final: 0.7536 (tp30) REVERT: B 45 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8270 (ttt-90) REVERT: B 61 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.3617 (mmp-170) REVERT: B 212 LYS cc_start: 0.8599 (pttt) cc_final: 0.8090 (pttp) REVERT: B 250 GLN cc_start: 0.8126 (pp30) cc_final: 0.7647 (pp30) REVERT: C 221 MET cc_start: 0.8430 (mtp) cc_final: 0.8136 (ptp) REVERT: D 5 ASP cc_start: 0.8012 (m-30) cc_final: 0.7782 (m-30) REVERT: D 173 MET cc_start: 0.9096 (ttt) cc_final: 0.8030 (ttt) REVERT: D 225 GLN cc_start: 0.9182 (mp10) cc_final: 0.8241 (mt0) REVERT: D 317 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7396 (tm-30) REVERT: E 20 ASP cc_start: 0.8211 (t0) cc_final: 0.7986 (t0) REVERT: E 109 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6084 (pt0) REVERT: F 148 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8090 (mttm) REVERT: H 97 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7707 (ptpp) REVERT: H 286 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8723 (mp) REVERT: I 16 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7824 (ttt180) REVERT: I 23 ASN cc_start: 0.8467 (t0) cc_final: 0.8254 (t0) REVERT: I 88 MET cc_start: 0.8898 (mtm) cc_final: 0.8549 (mtp) REVERT: I 196 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8381 (mt) REVERT: K 44 MET cc_start: 0.5834 (mmt) cc_final: 0.5552 (tpp) REVERT: K 78 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6672 (tm-30) REVERT: K 82 TYR cc_start: 0.5604 (p90) cc_final: 0.4927 (p90) REVERT: M 7 ARG cc_start: 0.8817 (ttt-90) cc_final: 0.8287 (ttt90) REVERT: M 238 TYR cc_start: 0.8752 (t80) cc_final: 0.8256 (t80) REVERT: O 86 MET cc_start: 0.1929 (mmt) cc_final: 0.1506 (mmm) outliers start: 131 outliers final: 78 residues processed: 434 average time/residue: 0.4599 time to fit residues: 336.0369 Evaluate side-chains 371 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 286 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 504 ARG Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 904 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 357 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 376 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS A 316 GLN A 349 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 ASN I 9 HIS I 218 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37323 Z= 0.235 Angle : 0.658 11.785 51374 Z= 0.336 Chirality : 0.042 0.321 5814 Planarity : 0.004 0.053 6199 Dihedral : 17.017 150.673 6605 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.32 % Favored : 93.53 % Rotamer: Outliers : 4.67 % Allowed : 15.85 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % 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: -1.27 (0.13), residues: 4206 helix: 0.13 (0.12), residues: 1768 sheet: -0.72 (0.21), residues: 545 loop : -1.82 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 43 HIS 0.009 0.001 HIS B 220 PHE 0.017 0.001 PHE M 73 TYR 0.022 0.002 TYR K 82 ARG 0.007 0.000 ARG H 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 305 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 322 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7727 (tp) REVERT: G 717 GLN cc_start: 0.3661 (tt0) cc_final: 0.2403 (mm-40) REVERT: G 837 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4998 (mt) REVERT: G 870 MET cc_start: 0.5112 (mmt) cc_final: 0.4564 (mmt) REVERT: G 906 PHE cc_start: 0.5420 (p90) cc_final: 0.3799 (t80) REVERT: G 937 ASP cc_start: 0.5034 (t70) cc_final: 0.3998 (p0) REVERT: A 235 ASN cc_start: 0.8287 (m110) cc_final: 0.7990 (m110) REVERT: A 239 PRO cc_start: 0.8795 (Cg_endo) cc_final: 0.8572 (Cg_exo) REVERT: A 308 GLU cc_start: 0.7863 (tp30) cc_final: 0.7567 (tp30) REVERT: B 45 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8347 (ttt-90) REVERT: B 61 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.3375 (mmp-170) REVERT: B 78 TRP cc_start: 0.2976 (OUTLIER) cc_final: 0.1349 (m100) REVERT: B 250 GLN cc_start: 0.8149 (pp30) cc_final: 0.7693 (pp30) REVERT: D 5 ASP cc_start: 0.8002 (m-30) cc_final: 0.7752 (m-30) REVERT: D 173 MET cc_start: 0.9179 (ttt) cc_final: 0.8058 (ttt) REVERT: D 225 GLN cc_start: 0.9185 (mp10) cc_final: 0.8279 (mt0) REVERT: D 317 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7352 (tm-30) REVERT: E 20 ASP cc_start: 0.8214 (t0) cc_final: 0.8008 (t0) REVERT: E 109 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6171 (pt0) REVERT: E 182 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8825 (t) REVERT: E 316 GLN cc_start: 0.8270 (pt0) cc_final: 0.8026 (pt0) REVERT: F 148 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8076 (mttm) REVERT: H 286 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8730 (mp) REVERT: I 23 ASN cc_start: 0.8447 (t0) cc_final: 0.8241 (t0) REVERT: I 88 MET cc_start: 0.8899 (mtm) cc_final: 0.8580 (mtp) REVERT: I 196 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8425 (mt) REVERT: K 78 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6704 (tm-30) REVERT: K 82 TYR cc_start: 0.5589 (p90) cc_final: 0.4847 (p90) REVERT: K 187 GLN cc_start: 0.8895 (mp10) cc_final: 0.8317 (mp10) REVERT: M 238 TYR cc_start: 0.8837 (t80) cc_final: 0.8503 (t80) REVERT: O 86 MET cc_start: 0.1959 (mmt) cc_final: 0.1543 (mmm) outliers start: 160 outliers final: 111 residues processed: 434 average time/residue: 0.4381 time to fit residues: 322.3909 Evaluate side-chains 400 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 280 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 504 ARG Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain G residue 904 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 88 MET Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 138 optimal weight: 0.5980 chunk 220 optimal weight: 0.0970 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 HIS A 349 ASN B 236 ASN C 236 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 238 ASN E 285 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37323 Z= 0.180 Angle : 0.639 11.921 51374 Z= 0.324 Chirality : 0.041 0.459 5814 Planarity : 0.004 0.052 6199 Dihedral : 16.933 149.105 6605 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 4.26 % Allowed : 16.87 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % 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: -1.05 (0.13), residues: 4206 helix: 0.35 (0.12), residues: 1758 sheet: -0.61 (0.21), residues: 551 loop : -1.73 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 43 HIS 0.010 0.001 HIS B 220 PHE 0.014 0.001 PHE M 73 TYR 0.020 0.001 TYR K 82 ARG 0.007 0.000 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 327 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.4972 (mtt-85) cc_final: 0.3790 (mmp80) REVERT: G 322 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7869 (tp) REVERT: G 717 GLN cc_start: 0.3452 (tt0) cc_final: 0.2196 (mm-40) REVERT: G 870 MET cc_start: 0.5050 (mmt) cc_final: 0.4479 (mmt) REVERT: G 906 PHE cc_start: 0.5238 (p90) cc_final: 0.3581 (t80) REVERT: G 937 ASP cc_start: 0.5043 (t70) cc_final: 0.3990 (p0) REVERT: A 133 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (pp) REVERT: A 180 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7530 (tt0) REVERT: A 235 ASN cc_start: 0.8316 (m110) cc_final: 0.7995 (m110) REVERT: A 239 PRO cc_start: 0.8799 (Cg_endo) cc_final: 0.8522 (Cg_exo) REVERT: A 308 GLU cc_start: 0.7787 (tp30) cc_final: 0.7462 (tp30) REVERT: B 45 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8323 (ttt-90) REVERT: B 61 ARG cc_start: 0.4893 (OUTLIER) cc_final: 0.3247 (mmp-170) REVERT: B 78 TRP cc_start: 0.2841 (OUTLIER) cc_final: 0.1265 (m100) REVERT: B 212 LYS cc_start: 0.8552 (pttt) cc_final: 0.8063 (pttp) REVERT: B 250 GLN cc_start: 0.8119 (pp30) cc_final: 0.7667 (pp30) REVERT: D 5 ASP cc_start: 0.7861 (m-30) cc_final: 0.7633 (m-30) REVERT: D 173 MET cc_start: 0.9077 (ttt) cc_final: 0.7931 (ttt) REVERT: D 225 GLN cc_start: 0.9141 (mp10) cc_final: 0.8203 (mt0) REVERT: D 317 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7358 (tm-30) REVERT: E 20 ASP cc_start: 0.8147 (t0) cc_final: 0.7859 (t70) REVERT: E 109 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6141 (pt0) REVERT: F 148 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8059 (mttm) REVERT: H 97 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7712 (ptpp) REVERT: I 88 MET cc_start: 0.8864 (mtm) cc_final: 0.8481 (mtp) REVERT: I 196 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8389 (mt) REVERT: K 78 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6661 (tm-30) REVERT: K 82 TYR cc_start: 0.5683 (p90) cc_final: 0.5146 (p90) REVERT: K 187 GLN cc_start: 0.8826 (mp10) cc_final: 0.8247 (mp10) REVERT: M 20 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7400 (mmt) REVERT: M 203 VAL cc_start: 0.9371 (m) cc_final: 0.9085 (p) REVERT: M 242 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9104 (tt) REVERT: O 86 MET cc_start: 0.1839 (mmt) cc_final: 0.1487 (mmm) outliers start: 146 outliers final: 92 residues processed: 439 average time/residue: 0.4471 time to fit residues: 332.3465 Evaluate side-chains 392 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 291 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain G residue 904 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 418 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 193 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS C 236 ASN C 272 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 238 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37323 Z= 0.260 Angle : 0.666 13.100 51374 Z= 0.339 Chirality : 0.042 0.489 5814 Planarity : 0.004 0.053 6199 Dihedral : 16.928 149.867 6599 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.65 % Rotamer: Outliers : 4.41 % Allowed : 17.40 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4206 helix: 0.42 (0.12), residues: 1751 sheet: -0.47 (0.22), residues: 543 loop : -1.66 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 43 HIS 0.007 0.001 HIS B 220 PHE 0.018 0.002 PHE F 204 TYR 0.023 0.002 TYR K 82 ARG 0.007 0.000 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 294 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.5059 (mtt-85) cc_final: 0.3823 (mmp80) REVERT: G 322 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7963 (tp) REVERT: G 717 GLN cc_start: 0.3445 (tt0) cc_final: 0.2183 (mm-40) REVERT: G 870 MET cc_start: 0.4952 (mmt) cc_final: 0.4343 (mmt) REVERT: G 906 PHE cc_start: 0.5149 (p90) cc_final: 0.3542 (t80) REVERT: G 937 ASP cc_start: 0.4985 (t70) cc_final: 0.3951 (p0) REVERT: A 133 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 138 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8974 (tt) REVERT: A 180 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7585 (tt0) REVERT: A 235 ASN cc_start: 0.8485 (m110) cc_final: 0.8183 (m110) REVERT: A 239 PRO cc_start: 0.8775 (Cg_endo) cc_final: 0.8560 (Cg_exo) REVERT: A 308 GLU cc_start: 0.7870 (tp30) cc_final: 0.7550 (tp30) REVERT: A 331 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: A 334 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8672 (tp) REVERT: B 45 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8353 (ttt-90) REVERT: B 61 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.3303 (mmp-170) REVERT: B 78 TRP cc_start: 0.2951 (OUTLIER) cc_final: 0.1353 (m100) REVERT: B 212 LYS cc_start: 0.8607 (pttt) cc_final: 0.8105 (pttp) REVERT: B 250 GLN cc_start: 0.8212 (pp30) cc_final: 0.7743 (pp30) REVERT: C 200 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: D 5 ASP cc_start: 0.8029 (m-30) cc_final: 0.7783 (m-30) REVERT: D 173 MET cc_start: 0.9226 (ttt) cc_final: 0.8005 (ttt) REVERT: D 214 ASN cc_start: 0.7615 (m-40) cc_final: 0.6855 (t0) REVERT: D 225 GLN cc_start: 0.9209 (mp10) cc_final: 0.8289 (mt0) REVERT: D 317 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 324 ARG cc_start: 0.7807 (mtm180) cc_final: 0.7289 (mtm-85) REVERT: E 20 ASP cc_start: 0.8183 (t0) cc_final: 0.7920 (t70) REVERT: E 109 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6110 (pt0) REVERT: E 182 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8877 (t) REVERT: F 20 ASP cc_start: 0.8425 (t0) cc_final: 0.8199 (t0) REVERT: F 43 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.8257 (t60) REVERT: F 148 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8006 (mttm) REVERT: H 97 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7812 (ptpp) REVERT: I 88 MET cc_start: 0.8895 (mtm) cc_final: 0.8599 (mtp) REVERT: I 196 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8485 (mt) REVERT: K 44 MET cc_start: 0.5794 (mmt) cc_final: 0.5524 (ptt) REVERT: K 78 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6635 (tm-30) REVERT: K 82 TYR cc_start: 0.5596 (p90) cc_final: 0.5263 (p90) REVERT: K 187 GLN cc_start: 0.8824 (mp10) cc_final: 0.8220 (mp10) REVERT: M 20 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7207 (mmt) REVERT: M 203 VAL cc_start: 0.9436 (m) cc_final: 0.9146 (p) REVERT: O 86 MET cc_start: 0.1818 (mmt) cc_final: 0.1459 (mmm) outliers start: 151 outliers final: 110 residues processed: 415 average time/residue: 0.4324 time to fit residues: 302.5305 Evaluate side-chains 404 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 280 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 82 optimal weight: 0.0000 chunk 81 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 284 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS C 236 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 37323 Z= 0.325 Angle : 0.701 15.501 51374 Z= 0.359 Chirality : 0.044 0.397 5814 Planarity : 0.005 0.054 6199 Dihedral : 17.016 150.960 6599 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.60 % Rotamer: Outliers : 4.50 % Allowed : 17.63 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.13), residues: 4206 helix: 0.32 (0.12), residues: 1750 sheet: -0.48 (0.22), residues: 555 loop : -1.67 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 43 HIS 0.009 0.001 HIS G 620 PHE 0.022 0.002 PHE F 204 TYR 0.025 0.002 TYR K 82 ARG 0.007 0.001 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 292 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.5054 (mtt-85) cc_final: 0.3764 (mmp80) REVERT: G 717 GLN cc_start: 0.3515 (tt0) cc_final: 0.2199 (mm-40) REVERT: G 870 MET cc_start: 0.4995 (mmt) cc_final: 0.4431 (mmt) REVERT: G 906 PHE cc_start: 0.5267 (p90) cc_final: 0.3819 (t80) REVERT: A 133 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8145 (pp) REVERT: A 138 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 196 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7121 (mmt) REVERT: A 235 ASN cc_start: 0.8520 (m110) cc_final: 0.8244 (m110) REVERT: A 239 PRO cc_start: 0.8835 (Cg_endo) cc_final: 0.8581 (Cg_exo) REVERT: A 308 GLU cc_start: 0.7927 (tp30) cc_final: 0.7570 (tp30) REVERT: A 331 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: A 334 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8727 (tp) REVERT: B 45 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8389 (ttt-90) REVERT: B 61 ARG cc_start: 0.4539 (OUTLIER) cc_final: 0.2923 (mmp-170) REVERT: B 78 TRP cc_start: 0.2999 (OUTLIER) cc_final: 0.1439 (m100) REVERT: B 250 GLN cc_start: 0.8226 (pp30) cc_final: 0.7782 (pp30) REVERT: C 173 MET cc_start: 0.8444 (ttm) cc_final: 0.8085 (ttm) REVERT: C 200 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: D 173 MET cc_start: 0.9214 (ttt) cc_final: 0.7968 (ttt) REVERT: D 214 ASN cc_start: 0.7500 (m-40) cc_final: 0.6790 (t0) REVERT: D 225 GLN cc_start: 0.9212 (mp10) cc_final: 0.8399 (mt0) REVERT: D 324 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7315 (mtm-85) REVERT: E 20 ASP cc_start: 0.8248 (t0) cc_final: 0.8003 (t70) REVERT: E 109 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6096 (pt0) REVERT: E 182 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8947 (t) REVERT: E 214 ASN cc_start: 0.7852 (t0) cc_final: 0.7589 (t0) REVERT: F 20 ASP cc_start: 0.8446 (t0) cc_final: 0.8232 (t0) REVERT: F 43 TRP cc_start: 0.8820 (OUTLIER) cc_final: 0.8418 (t60) REVERT: F 148 LYS cc_start: 0.8631 (ptpt) cc_final: 0.8038 (mttm) REVERT: F 202 ASP cc_start: 0.8732 (t0) cc_final: 0.8446 (t0) REVERT: H 68 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: H 97 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7836 (ptpp) REVERT: I 88 MET cc_start: 0.8953 (mtm) cc_final: 0.8642 (mtp) REVERT: I 196 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8525 (mt) REVERT: K 78 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6664 (tm-30) REVERT: K 82 TYR cc_start: 0.5885 (p90) cc_final: 0.5432 (p90) REVERT: K 187 GLN cc_start: 0.8846 (mp10) cc_final: 0.8237 (mp10) REVERT: M 203 VAL cc_start: 0.9489 (m) cc_final: 0.9217 (p) REVERT: M 238 TYR cc_start: 0.8906 (t80) cc_final: 0.8570 (t80) REVERT: O 86 MET cc_start: 0.1988 (mmt) cc_final: 0.1595 (mmm) outliers start: 154 outliers final: 115 residues processed: 415 average time/residue: 0.4474 time to fit residues: 315.9100 Evaluate side-chains 400 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 271 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 657 VAL Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 695 HIS Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 776 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 0.8980 chunk 400 optimal weight: 0.0970 chunk 365 optimal weight: 5.9990 chunk 389 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 352 optimal weight: 0.0670 chunk 368 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 236 ASN C 236 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37323 Z= 0.170 Angle : 0.651 14.146 51374 Z= 0.325 Chirality : 0.041 0.398 5814 Planarity : 0.004 0.049 6199 Dihedral : 16.869 149.086 6599 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 3.36 % Allowed : 18.91 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4206 helix: 0.50 (0.12), residues: 1757 sheet: -0.32 (0.22), residues: 537 loop : -1.58 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 43 HIS 0.013 0.001 HIS B 220 PHE 0.019 0.001 PHE K 148 TYR 0.019 0.001 TYR E 14 ARG 0.009 0.000 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 343 time to evaluate : 4.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.4995 (mtt-85) cc_final: 0.3792 (mmp80) REVERT: G 320 ASP cc_start: 0.7364 (t0) cc_final: 0.7074 (t0) REVERT: G 526 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7201 (t0) REVERT: G 717 GLN cc_start: 0.2957 (tt0) cc_final: 0.1828 (mm-40) REVERT: G 794 LEU cc_start: 0.8233 (tt) cc_final: 0.7848 (tp) REVERT: G 870 MET cc_start: 0.5001 (mmt) cc_final: 0.4436 (mmt) REVERT: G 906 PHE cc_start: 0.5058 (p90) cc_final: 0.3485 (t80) REVERT: A 138 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8918 (tt) REVERT: A 180 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7599 (tt0) REVERT: A 235 ASN cc_start: 0.8393 (m110) cc_final: 0.8086 (m110) REVERT: A 308 GLU cc_start: 0.7814 (tp30) cc_final: 0.7456 (tp30) REVERT: A 334 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8562 (tp) REVERT: B 45 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8402 (ttt-90) REVERT: B 61 ARG cc_start: 0.4356 (OUTLIER) cc_final: 0.2914 (mmp-170) REVERT: B 78 TRP cc_start: 0.2695 (OUTLIER) cc_final: 0.1170 (m100) REVERT: B 212 LYS cc_start: 0.8496 (pttt) cc_final: 0.8030 (pttp) REVERT: B 250 GLN cc_start: 0.8147 (pp30) cc_final: 0.7712 (pp30) REVERT: C 200 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: D 5 ASP cc_start: 0.7812 (m-30) cc_final: 0.7583 (m-30) REVERT: D 158 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 173 MET cc_start: 0.9090 (ttt) cc_final: 0.7848 (ttt) REVERT: D 317 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7307 (tm-30) REVERT: D 324 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7303 (mtm-85) REVERT: E 20 ASP cc_start: 0.8138 (t0) cc_final: 0.7856 (t70) REVERT: E 182 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8786 (t) REVERT: F 20 ASP cc_start: 0.8321 (t0) cc_final: 0.8094 (t0) REVERT: F 148 LYS cc_start: 0.8599 (ptpt) cc_final: 0.7971 (mttm) REVERT: F 188 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: F 202 ASP cc_start: 0.8710 (t0) cc_final: 0.8405 (t0) REVERT: H 97 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7703 (ptpp) REVERT: I 88 MET cc_start: 0.8820 (mtm) cc_final: 0.8477 (mtp) REVERT: I 196 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8468 (mt) REVERT: I 227 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8185 (tm-30) REVERT: K 78 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6628 (tm-30) REVERT: K 187 GLN cc_start: 0.8764 (mp10) cc_final: 0.8147 (mp10) REVERT: M 110 ASP cc_start: 0.7204 (t0) cc_final: 0.6780 (t70) REVERT: M 203 VAL cc_start: 0.9363 (m) cc_final: 0.9103 (p) REVERT: M 242 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9137 (tt) outliers start: 115 outliers final: 83 residues processed: 432 average time/residue: 0.4480 time to fit residues: 329.1646 Evaluate side-chains 391 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 297 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 657 VAL Chi-restraints excluded: chain G residue 800 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 164 TYR Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 3.9990 chunk 412 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 286 optimal weight: 0.3980 chunk 432 optimal weight: 0.5980 chunk 397 optimal weight: 5.9990 chunk 344 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37323 Z= 0.188 Angle : 0.652 13.115 51374 Z= 0.327 Chirality : 0.041 0.322 5814 Planarity : 0.004 0.050 6199 Dihedral : 16.820 148.361 6597 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 2.95 % Allowed : 19.85 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4206 helix: 0.57 (0.13), residues: 1765 sheet: -0.21 (0.22), residues: 528 loop : -1.53 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 43 HIS 0.009 0.001 HIS B 220 PHE 0.019 0.001 PHE K 148 TYR 0.030 0.001 TYR M 238 ARG 0.009 0.000 ARG M 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 309 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.5066 (mtt-85) cc_final: 0.3828 (mmp80) REVERT: G 320 ASP cc_start: 0.7365 (t0) cc_final: 0.7137 (t0) REVERT: G 344 MET cc_start: 0.7484 (tmm) cc_final: 0.6840 (ttt) REVERT: G 525 VAL cc_start: 0.9101 (p) cc_final: 0.8879 (m) REVERT: G 717 GLN cc_start: 0.2633 (tt0) cc_final: 0.1514 (mm-40) REVERT: G 794 LEU cc_start: 0.8258 (tt) cc_final: 0.7962 (tp) REVERT: G 870 MET cc_start: 0.5001 (mmt) cc_final: 0.4446 (mmt) REVERT: G 906 PHE cc_start: 0.5055 (p90) cc_final: 0.3564 (t80) REVERT: G 937 ASP cc_start: 0.5064 (t70) cc_final: 0.3859 (p0) REVERT: A 138 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 180 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7637 (tt0) REVERT: A 196 MET cc_start: 0.7191 (mtp) cc_final: 0.6647 (mtt) REVERT: A 235 ASN cc_start: 0.8403 (m110) cc_final: 0.8130 (m110) REVERT: A 308 GLU cc_start: 0.7832 (tp30) cc_final: 0.7489 (tp30) REVERT: A 334 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8513 (tp) REVERT: B 45 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8322 (ttt-90) REVERT: B 61 ARG cc_start: 0.4079 (OUTLIER) cc_final: 0.2632 (mmp-170) REVERT: B 78 TRP cc_start: 0.2798 (OUTLIER) cc_final: 0.1205 (m100) REVERT: B 212 LYS cc_start: 0.8521 (pttt) cc_final: 0.7980 (pttp) REVERT: B 250 GLN cc_start: 0.8181 (pp30) cc_final: 0.7736 (pp30) REVERT: B 317 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 200 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: D 158 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 173 MET cc_start: 0.9175 (ttt) cc_final: 0.7915 (ttt) REVERT: D 317 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7338 (tm-30) REVERT: D 324 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7031 (mtm-85) REVERT: E 20 ASP cc_start: 0.8130 (t0) cc_final: 0.7847 (t70) REVERT: E 182 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8827 (t) REVERT: F 20 ASP cc_start: 0.8352 (t0) cc_final: 0.8096 (t0) REVERT: F 148 LYS cc_start: 0.8771 (ptpt) cc_final: 0.8444 (mmtp) REVERT: F 188 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: H 97 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7766 (ptpp) REVERT: I 88 MET cc_start: 0.8842 (mtm) cc_final: 0.8517 (mtp) REVERT: I 196 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8495 (mt) REVERT: K 78 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6567 (tm-30) REVERT: K 187 GLN cc_start: 0.8717 (mp10) cc_final: 0.8106 (mp10) REVERT: M 110 ASP cc_start: 0.7374 (t0) cc_final: 0.6947 (t70) REVERT: M 203 VAL cc_start: 0.9392 (m) cc_final: 0.9124 (p) REVERT: M 242 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9148 (tt) REVERT: O 86 MET cc_start: 0.3398 (mmm) cc_final: 0.2851 (mmm) outliers start: 101 outliers final: 81 residues processed: 387 average time/residue: 0.4491 time to fit residues: 296.8164 Evaluate side-chains 382 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 291 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 443 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 657 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 164 TYR Chi-restraints excluded: chain O residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 105 optimal weight: 0.0070 chunk 317 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 238 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.124330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093026 restraints weight = 83002.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094337 restraints weight = 45592.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094491 restraints weight = 29234.981| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37323 Z= 0.233 Angle : 0.666 13.915 51374 Z= 0.334 Chirality : 0.042 0.350 5814 Planarity : 0.004 0.052 6199 Dihedral : 16.846 148.124 6595 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 3.06 % Allowed : 19.82 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4206 helix: 0.53 (0.13), residues: 1768 sheet: -0.18 (0.22), residues: 535 loop : -1.48 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 43 HIS 0.009 0.001 HIS B 220 PHE 0.021 0.002 PHE K 148 TYR 0.032 0.001 TYR M 238 ARG 0.012 0.000 ARG A 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7184.54 seconds wall clock time: 131 minutes 32.10 seconds (7892.10 seconds total)